Query 038783
Match_columns 76
No_of_seqs 110 out of 932
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 03:14:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038783.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038783hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00432 MADS MADS domain. 100.0 1.4E-29 3.1E-34 151.2 5.0 59 18-76 1-59 (59)
2 KOG0014 MADS box transcription 100.0 9.1E-30 2E-34 174.3 3.6 60 17-76 1-60 (195)
3 cd00265 MADS_MEF2_like MEF2 (m 100.0 3.8E-29 8.1E-34 155.1 3.8 59 18-76 1-59 (77)
4 cd00120 MADS MADS: MCM1, Agamo 99.9 1.3E-28 2.8E-33 147.0 4.2 59 18-76 1-59 (59)
5 cd00266 MADS_SRF_like SRF-like 99.9 2E-27 4.4E-32 148.9 3.9 59 18-76 1-59 (83)
6 PF00319 SRF-TF: SRF-type tran 99.9 4.7E-27 1E-31 137.0 0.5 51 25-75 1-51 (51)
7 KOG0015 Regulator of arginine 99.9 6.3E-23 1.4E-27 154.7 4.8 69 8-76 53-121 (338)
8 COG5068 ARG80 Regulator of arg 99.6 2.5E-15 5.4E-20 116.7 4.1 61 16-76 80-140 (412)
9 PF13540 RCC1_2: Regulator of 83.4 1.2 2.5E-05 22.5 2.0 24 52-76 3-26 (30)
10 PF09151 DUF1936: Domain of un 75.5 3.7 7.9E-05 22.1 2.4 24 50-73 2-25 (36)
11 cd00472 Ribosomal_L24e_L24 Rib 60.0 8 0.00017 22.5 1.9 27 50-76 4-34 (54)
12 PRK14891 50S ribosomal protein 59.6 6.3 0.00014 27.0 1.6 27 50-76 5-35 (131)
13 PRK00807 50S ribosomal protein 55.5 14 0.00031 21.1 2.4 27 50-76 2-32 (52)
14 PF09941 DUF2173: Uncharacteri 55.0 16 0.00034 24.2 2.8 27 47-74 2-28 (108)
15 PF01246 Ribosomal_L24e: Ribos 54.1 12 0.00026 22.9 2.0 27 50-76 4-34 (71)
16 PF07676 PD40: WD40-like Beta 53.1 16 0.00034 18.4 2.2 18 58-75 10-27 (39)
17 TIGR01916 F420_cofE F420-0:gam 52.1 11 0.00024 28.0 1.9 27 49-75 133-159 (243)
18 KOG0184 20S proteasome, regula 49.2 11 0.00023 28.4 1.5 21 52-72 3-23 (254)
19 PF04945 YHS: YHS domain; Int 48.9 13 0.00029 20.1 1.5 22 55-76 6-30 (47)
20 COG2075 RPL24A Ribosomal prote 47.7 20 0.00044 21.9 2.3 27 50-76 4-34 (66)
21 PHA02757 hypothetical protein; 47.6 23 0.0005 21.9 2.5 18 58-75 46-64 (75)
22 PRK13293 F420-0--gamma-glutamy 45.4 16 0.00034 27.3 1.9 26 49-74 134-159 (245)
23 PF10584 Proteasome_A_N: Prote 43.6 4.4 9.6E-05 20.0 -0.9 12 61-72 5-16 (23)
24 COG4831 Roadblock/LC7 domain [ 42.4 32 0.0007 22.8 2.8 30 45-75 2-31 (109)
25 PTZ00033 60S ribosomal protein 40.7 19 0.00042 24.5 1.6 27 50-76 4-38 (125)
26 PF00383 dCMP_cyt_deam_1: Cyti 39.5 35 0.00075 20.5 2.5 31 44-74 7-41 (102)
27 cd01057 AAMH_A Aromatic and Al 36.3 24 0.00052 28.3 1.7 26 51-76 382-416 (465)
28 PRK09555 feoA ferrous iron tra 35.9 75 0.0016 19.1 3.5 32 42-73 20-51 (74)
29 COG5000 NtrY Signal transducti 33.0 33 0.00071 29.3 2.1 23 52-74 374-396 (712)
30 cd01284 Riboflavin_deaminase-r 32.3 59 0.0013 21.0 2.8 29 46-74 2-36 (115)
31 PRK13294 F420-0--gamma-glutamy 32.3 33 0.00071 27.3 1.9 26 49-74 134-159 (448)
32 COG0139 HisI Phosphoribosyl-AM 31.9 22 0.00048 23.8 0.7 26 43-68 69-94 (111)
33 KOG0182 20S proteasome, regula 31.2 48 0.001 24.9 2.5 20 53-72 5-24 (246)
34 COG5184 ATS1 Alpha-tubulin sup 30.9 47 0.001 27.2 2.6 24 51-75 179-202 (476)
35 PRK09732 hypothetical protein; 30.8 69 0.0015 21.5 3.0 29 45-73 16-44 (134)
36 PF14263 DUF4354: Domain of un 30.3 18 0.00038 24.5 0.1 43 26-73 40-82 (124)
37 cd01363 Motor_domain Myosin an 30.1 48 0.001 22.4 2.2 22 52-73 18-41 (186)
38 PF01996 F420_ligase: F420-0:G 29.6 8.5 0.00018 27.8 -1.7 26 49-74 141-166 (228)
39 PF02145 Rap_GAP: Rap/ran-GAP; 29.6 28 0.00061 24.2 1.0 20 55-74 79-98 (188)
40 PF01502 PRA-CH: Phosphoribosy 28.6 24 0.00052 21.9 0.5 27 43-69 37-63 (75)
41 cd06404 PB1_aPKC PB1 domain is 27.8 94 0.002 19.7 3.1 35 41-75 22-57 (83)
42 PF11232 Med25: Mediator compl 27.7 69 0.0015 22.3 2.7 19 53-71 109-127 (152)
43 PF06020 Roughex: Drosophila r 27.5 33 0.00071 26.8 1.1 15 52-66 183-197 (334)
44 cd09011 Glo_EDI_BRP_like_23 Th 27.2 74 0.0016 19.0 2.5 18 59-76 102-119 (120)
45 cd01285 nucleoside_deaminase N 27.2 87 0.0019 19.5 2.9 22 54-75 14-35 (109)
46 smart00782 PhnA_Zn_Ribbon PhnA 27.2 31 0.00067 19.5 0.7 22 44-65 2-23 (47)
47 PHA02773 hypothetical protein; 26.8 1.5E+02 0.0032 19.6 3.9 35 40-74 24-59 (112)
48 cd07242 Glo_EDI_BRP_like_6 Thi 26.3 66 0.0014 19.3 2.2 17 60-76 112-128 (128)
49 cd08356 Glo_EDI_BRP_like_17 Th 25.5 88 0.0019 18.9 2.6 17 59-75 97-113 (113)
50 cd07246 Glo_EDI_BRP_like_8 Thi 24.3 1.2E+02 0.0026 17.7 3.0 19 58-76 104-122 (122)
51 cd08350 BLMT_like BLMT, a bleo 23.6 96 0.0021 18.6 2.6 18 59-76 102-119 (120)
52 PF09816 EAF: RNA polymerase I 23.4 80 0.0017 20.0 2.2 17 56-72 76-92 (109)
53 COG5068 ARG80 Regulator of arg 23.3 40 0.00087 27.1 0.9 45 24-74 18-62 (412)
54 COG5184 ATS1 Alpha-tubulin sup 23.2 91 0.002 25.6 2.9 29 47-76 230-258 (476)
55 cd01372 KISc_KIF4 Kinesin moto 23.1 61 0.0013 24.0 1.8 23 52-74 68-92 (341)
56 PF08796 DUF1797: Protein of u 22.9 1.1E+02 0.0024 18.6 2.6 19 54-72 23-41 (67)
57 cd01365 KISc_KIF1A_KIF1B Kines 22.7 79 0.0017 23.7 2.4 22 52-73 83-106 (356)
58 smart00484 XPGI Xeroderma pigm 22.2 68 0.0015 19.3 1.6 27 49-75 16-42 (73)
59 PF13252 DUF4043: Protein of u 21.8 44 0.00095 25.8 0.9 28 46-73 269-298 (341)
60 cd01854 YjeQ_engC YjeQ/EngC. 21.5 45 0.00097 24.4 0.8 41 26-70 52-92 (287)
61 PF13186 SPASM: Iron-sulfur cl 21.4 85 0.0018 16.7 1.8 19 55-73 1-19 (64)
62 KOG0712 Molecular chaperone (D 21.4 1.2E+02 0.0025 23.7 3.1 39 34-75 244-285 (337)
63 PF15119 APOC4: Apolipoprotein 21.1 45 0.00097 21.8 0.7 20 37-56 75-96 (99)
64 cd01376 KISc_KID_like Kinesin 20.8 91 0.002 23.0 2.4 22 52-73 75-98 (319)
65 PF04873 EIN3: Ethylene insens 20.6 33 0.00072 26.8 0.0 38 39-76 51-89 (354)
66 cd07261 Glo_EDI_BRP_like_11 Th 20.1 1.2E+02 0.0027 17.7 2.5 16 60-75 99-114 (114)
No 1
>smart00432 MADS MADS domain.
Probab=99.96 E-value=1.4e-29 Score=151.15 Aligned_cols=59 Identities=81% Similarity=1.157 Sum_probs=58.1
Q ss_pred cccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783 18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76 (76)
Q Consensus 18 gRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~ 76 (76)
||+||+|++|+|++.|++||+||+.||+|||+|||+||||+||+|||+|+|++|+|++|
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 89999999999999999999999999999999999999999999999999999999986
No 2
>KOG0014 consensus MADS box transcription factor [Transcription]
Probab=99.96 E-value=9.1e-30 Score=174.27 Aligned_cols=60 Identities=73% Similarity=1.158 Sum_probs=58.8
Q ss_pred ccccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783 17 IGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76 (76)
Q Consensus 17 mgRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~ 76 (76)
|||+||+|++|+|+..|++||+||+.||||||+||||||||+||+|||+|+|++|.|+++
T Consensus 1 M~R~ki~i~~Ien~~~RqvTFsKRr~GL~KKA~ELsvLCd~eiavIifsp~~~~~~~~~~ 60 (195)
T KOG0014|consen 1 MGRGKIEIKRIENESSRQVTFSKRRNGLFKKASELSVLCDAEIAVIVFSPSGKLYEFGSS 60 (195)
T ss_pred CCCCccceeeccccchhhhhhHHHHhhHHHHHHHHHHhcCCeEEEEEECCCCCccccCCc
Confidence 899999999999999999999999999999999999999999999999999999999874
No 3
>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=99.95 E-value=3.8e-29 Score=155.11 Aligned_cols=59 Identities=83% Similarity=1.220 Sum_probs=57.9
Q ss_pred cccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783 18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76 (76)
Q Consensus 18 gRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~ 76 (76)
||+||+|++|+|+..|++||+||+.||||||.|||+||||+||+|||+|+|++|+|+++
T Consensus 1 gr~ki~i~~i~~~~~r~~tf~kR~~gl~kKa~Els~Lc~~~v~lvv~sp~gk~~~f~s~ 59 (77)
T cd00265 1 GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSP 59 (77)
T ss_pred CCCcceeEEecCccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCCCceEEecCC
Confidence 89999999999999999999999999999999999999999999999999999999985
No 4
>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=1.3e-28 Score=146.95 Aligned_cols=59 Identities=78% Similarity=1.149 Sum_probs=57.8
Q ss_pred cccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783 18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76 (76)
Q Consensus 18 gRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~ 76 (76)
||+||+|++|+|+..|++||+||+.||+|||+|||+|||++||+|||+|+|++++|+++
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 79999999999999999999999999999999999999999999999999999999975
No 5
>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=99.94 E-value=2e-27 Score=148.94 Aligned_cols=59 Identities=63% Similarity=0.947 Sum_probs=57.2
Q ss_pred cccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783 18 GRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76 (76)
Q Consensus 18 gRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~ 76 (76)
||+||+|++|+|+..|++||+||+.||+|||+|||+|||++||+|||+|+|+.++|+++
T Consensus 1 gr~Ki~i~~I~~~~~R~~tf~KRk~gl~kKa~ELs~Lc~~~v~~iv~sp~~~~~~~~~~ 59 (83)
T cd00266 1 GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPS 59 (83)
T ss_pred CCccceeEEeeccchhhhhHHHhhhhHHHHHHHHHHhhCCcEEEEEECCCCCcceecCc
Confidence 79999999999999999999999999999999999999999999999999999999864
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=99.92 E-value=4.7e-27 Score=137.03 Aligned_cols=51 Identities=61% Similarity=1.001 Sum_probs=47.0
Q ss_pred EEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccC
Q 038783 25 KRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75 (76)
Q Consensus 25 k~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s 75 (76)
++|+|+..|++||+||+.||+|||+|||+|||++||||||+|+|++|+|+|
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 579999999999999999999999999999999999999999999999987
No 7
>KOG0015 consensus Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.87 E-value=6.3e-23 Score=154.65 Aligned_cols=69 Identities=43% Similarity=0.683 Sum_probs=65.0
Q ss_pred CCCCcccccccccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783 8 PESSSQSKKIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76 (76)
Q Consensus 8 ~~~~~~~k~mgRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~ 76 (76)
......+++.||+||+|+||+|+..|.+||+|||.||||||+||++|+|.+|.|+|.+++|.+|+|+++
T Consensus 53 ~~~~~~k~~~gr~kik~eyIenK~rR~~tFSKRK~GImKKAyELs~LTGtqVllLVaSEtGhVyTFaTp 121 (338)
T KOG0015|consen 53 SQKDGGKKTTGRVKIKMEYIENKLRRYVTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATP 121 (338)
T ss_pred cccCCCccccceeeccchhhcccceeeeeehhhhhhhHHHHHHhhhcccceEEEEEEecCcceEEeccc
Confidence 335567888999999999999999999999999999999999999999999999999999999999985
No 8
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.56 E-value=2.5e-15 Score=116.65 Aligned_cols=61 Identities=44% Similarity=0.635 Sum_probs=59.5
Q ss_pred cccccceeeEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783 16 KIGRGKIEIKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYANN 76 (76)
Q Consensus 16 ~mgRkKi~ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s~ 76 (76)
.|||++|.|.+|+|+.+|.+||.||+.||+|||.||++|+|.+|.++|.+++|.+|+|+++
T Consensus 80 ~~~~~~~~is~i~nk~~r~vtf~Krk~gI~kka~ElsvLt~~~vl~lvise~g~v~tf~tp 140 (412)
T COG5068 80 SVTGRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTTP 140 (412)
T ss_pred ccccccCCcccccCcccccchhhhhhhhhhhhhhhhhhccCCceEEEEecCCCceeeecCC
Confidence 6889999999999999999999999999999999999999999999999999999999975
No 9
>PF13540 RCC1_2: Regulator of chromosome condensation (RCC1) repeat; PDB: 3QI0_D 1JTD_B 3QHY_B.
Probab=83.43 E-value=1.2 Score=22.51 Aligned_cols=24 Identities=21% Similarity=0.466 Sum_probs=16.8
Q ss_pred ccccCceEEEEEEcCCCcEEEccCC
Q 038783 52 SVLCDAEVALIVFSSRGRLYEYANN 76 (76)
Q Consensus 52 s~Lcg~~v~liv~~~~gk~~~f~s~ 76 (76)
++-||....+++.+ +|++|.|+.+
T Consensus 3 ~ia~G~~ht~al~~-~g~v~~wG~n 26 (30)
T PF13540_consen 3 QIACGGYHTCALTS-DGEVYCWGDN 26 (30)
T ss_dssp EEEEESSEEEEEE--TTEEEEEE--
T ss_pred EEEecCCEEEEEEc-CCCEEEEcCC
Confidence 46678787777765 6999999875
No 10
>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=75.48 E-value=3.7 Score=22.13 Aligned_cols=24 Identities=21% Similarity=0.438 Sum_probs=17.4
Q ss_pred hhccccCceEEEEEEcCCCcEEEc
Q 038783 50 ELSVLCDAEVALIVFSSRGRLYEY 73 (76)
Q Consensus 50 ELs~Lcg~~v~liv~~~~gk~~~f 73 (76)
.|+--||+-|.+.||+..|.+-.|
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 467789999999999999976655
No 11
>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=59.98 E-value=8 Score=22.51 Aligned_cols=27 Identities=11% Similarity=0.502 Sum_probs=20.0
Q ss_pred hhccccCceE----EEEEEcCCCcEEEccCC
Q 038783 50 ELSVLCDAEV----ALIVFSSRGRLYEYANN 76 (76)
Q Consensus 50 ELs~Lcg~~v----~liv~~~~gk~~~f~s~ 76 (76)
|+|.-||-+| ....+-.||++|.|+|+
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~F~s~ 34 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFRFCSS 34 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEEEECH
Confidence 6777788877 44555668999999874
No 12
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=59.65 E-value=6.3 Score=27.03 Aligned_cols=27 Identities=7% Similarity=0.261 Sum_probs=21.2
Q ss_pred hhccccCceE----EEEEEcCCCcEEEccCC
Q 038783 50 ELSVLCDAEV----ALIVFSSRGRLYEYANN 76 (76)
Q Consensus 50 ELs~Lcg~~v----~liv~~~~gk~~~f~s~ 76 (76)
++|..||..| ..+.+-.+|++|.|+|+
T Consensus 5 e~CsFcG~kIyPG~G~~fVR~DGkvf~Fcss 35 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMFVRKDGTVLHFVDS 35 (131)
T ss_pred eeecCcCCcccCCCCcEEEecCCCEEEEecH
Confidence 5788888887 45666778999999974
No 13
>PRK00807 50S ribosomal protein L24e; Validated
Probab=55.54 E-value=14 Score=21.07 Aligned_cols=27 Identities=11% Similarity=0.388 Sum_probs=19.4
Q ss_pred hhccccCceEE----EEEEcCCCcEEEccCC
Q 038783 50 ELSVLCDAEVA----LIVFSSRGRLYEYANN 76 (76)
Q Consensus 50 ELs~Lcg~~v~----liv~~~~gk~~~f~s~ 76 (76)
+++.-||-+|- .+.+-.||++|.|+|+
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~Fcs~ 32 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILYFCSS 32 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEEEeCH
Confidence 45677887774 4445568999999884
No 14
>PF09941 DUF2173: Uncharacterized conserved protein (DUF2173); InterPro: IPR018685 This family of various hypothetical prokaryotic proteins has no known function.
Probab=55.04 E-value=16 Score=24.16 Aligned_cols=27 Identities=33% Similarity=0.317 Sum_probs=20.9
Q ss_pred hhhhhccccCceEEEEEEcCCCcEEEcc
Q 038783 47 KAYELSVLCDAEVALIVFSSRGRLYEYA 74 (76)
Q Consensus 47 Ka~ELs~Lcg~~v~liv~~~~gk~~~f~ 74 (76)
+..+|..|.||-+ ...|+++|++..|-
T Consensus 2 ~l~~Lm~lpGv~A-Ag~Fs~~G~l~e~~ 28 (108)
T PF09941_consen 2 KLDKLMKLPGVVA-AGEFSDDGKLVEYK 28 (108)
T ss_pred cHHHhhcCCCeEE-EEEECCCCeEEeee
Confidence 3468888888855 56789999998873
No 15
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=54.08 E-value=12 Score=22.93 Aligned_cols=27 Identities=7% Similarity=0.324 Sum_probs=17.5
Q ss_pred hhccccCceE----EEEEEcCCCcEEEccCC
Q 038783 50 ELSVLCDAEV----ALIVFSSRGRLYEYANN 76 (76)
Q Consensus 50 ELs~Lcg~~v----~liv~~~~gk~~~f~s~ 76 (76)
|+|.-||-.| ..+.+-.||++|.|+|.
T Consensus 4 ~~C~Fsg~~I~PG~G~~~Vr~DG~v~~F~s~ 34 (71)
T PF01246_consen 4 EKCSFSGYKIYPGHGKMYVRNDGKVFYFCSS 34 (71)
T ss_dssp EE-TTT-SEE-SSSSEEEE-TTS-EEEESSH
T ss_pred EEecccCCccCCCCCeEEEecCCCeEEEeCH
Confidence 6778888887 45566778999999873
No 16
>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=53.09 E-value=16 Score=18.43 Aligned_cols=18 Identities=11% Similarity=0.263 Sum_probs=13.7
Q ss_pred eEEEEEEcCCCcEEEccC
Q 038783 58 EVALIVFSSRGRLYEYAN 75 (76)
Q Consensus 58 ~v~liv~~~~gk~~~f~s 75 (76)
.-.-..++|+|+...|++
T Consensus 10 ~~~~p~~SpDGk~i~f~s 27 (39)
T PF07676_consen 10 DDGSPAWSPDGKYIYFTS 27 (39)
T ss_dssp SEEEEEE-TTSSEEEEEE
T ss_pred cccCEEEecCCCEEEEEe
Confidence 456678899999999876
No 17
>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=52.14 E-value=11 Score=28.03 Aligned_cols=27 Identities=22% Similarity=0.391 Sum_probs=22.4
Q ss_pred hhhccccCceEEEEEEcCCCcEEEccC
Q 038783 49 YELSVLCDAEVALIVFSSRGRLYEYAN 75 (76)
Q Consensus 49 ~ELs~Lcg~~v~liv~~~~gk~~~f~s 75 (76)
.+|.-.+|++|++||++..|++|--+.
T Consensus 133 ~~l~~~~g~~v~VIItDt~gr~~R~G~ 159 (243)
T TIGR01916 133 RGLRELTGVDVGVIITDTNGRPFREGQ 159 (243)
T ss_pred HHHHHHHCCCEEEEEECCCCCccccCC
Confidence 456778999999999999999886553
No 18
>KOG0184 consensus 20S proteasome, regulatory subunit alpha type PSMA3/PRE10 [Posttranslational modification, protein turnover, chaperones]
Probab=49.25 E-value=11 Score=28.39 Aligned_cols=21 Identities=24% Similarity=0.479 Sum_probs=18.4
Q ss_pred ccccCceEEEEEEcCCCcEEE
Q 038783 52 SVLCDAEVALIVFSSRGRLYE 72 (76)
Q Consensus 52 s~Lcg~~v~liv~~~~gk~~~ 72 (76)
||-+|-|.+..+|+|+|++|+
T Consensus 3 sIGtGyDls~s~fSpdGrvfQ 23 (254)
T KOG0184|consen 3 SIGTGYDLSASTFSPDGRVFQ 23 (254)
T ss_pred cccccccccceeeCCCCceeh
Confidence 566889999999999999985
No 19
>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=48.94 E-value=13 Score=20.10 Aligned_cols=22 Identities=27% Similarity=0.549 Sum_probs=14.2
Q ss_pred cCceE---EEEEEcCCCcEEEccCC
Q 038783 55 CDAEV---ALIVFSSRGRLYEYANN 76 (76)
Q Consensus 55 cg~~v---~liv~~~~gk~~~f~s~ 76 (76)
||..| +-..+.-+|+.|-|+|.
T Consensus 6 cg~~v~~~~~~~~~y~G~~Y~FCS~ 30 (47)
T PF04945_consen 6 CGMKVPGNAAYSVEYNGRTYYFCSE 30 (47)
T ss_dssp GG-BE-----EEEEETTEEEEESSH
T ss_pred CCCEEccCccEEEEECCEEEEEcCH
Confidence 56666 55556668999999983
No 20
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=47.73 E-value=20 Score=21.92 Aligned_cols=27 Identities=7% Similarity=0.530 Sum_probs=20.4
Q ss_pred hhccccCceE----EEEEEcCCCcEEEccCC
Q 038783 50 ELSVLCDAEV----ALIVFSSRGRLYEYANN 76 (76)
Q Consensus 50 ELs~Lcg~~v----~liv~~~~gk~~~f~s~ 76 (76)
+-|.-||.+| .++.+-.||+++-|+|+
T Consensus 4 ~~CsFcG~~I~PGtG~m~Vr~Dg~v~~Fcss 34 (66)
T COG2075 4 RVCSFCGKKIEPGTGIMYVRNDGKVLRFCSS 34 (66)
T ss_pred eEecCcCCccCCCceEEEEecCCeEEEEech
Confidence 3466788877 56666778999999985
No 21
>PHA02757 hypothetical protein; Provisional
Probab=47.62 E-value=23 Score=21.95 Aligned_cols=18 Identities=17% Similarity=0.433 Sum_probs=15.2
Q ss_pred eEEEEEEcCC-CcEEEccC
Q 038783 58 EVALIVFSSR-GRLYEYAN 75 (76)
Q Consensus 58 ~v~liv~~~~-gk~~~f~s 75 (76)
.+|+|=.+++ |.+++|+.
T Consensus 46 K~CiiE~de~sGml~s~C~ 64 (75)
T PHA02757 46 KACIIEIDEDSGMLFSQCD 64 (75)
T ss_pred ceEEEEEcCCCCcEEEecC
Confidence 5899989887 99999874
No 22
>PRK13293 F420-0--gamma-glutamyl ligase; Reviewed
Probab=45.36 E-value=16 Score=27.26 Aligned_cols=26 Identities=23% Similarity=0.373 Sum_probs=21.7
Q ss_pred hhhccccCceEEEEEEcCCCcEEEcc
Q 038783 49 YELSVLCDAEVALIVFSSRGRLYEYA 74 (76)
Q Consensus 49 ~ELs~Lcg~~v~liv~~~~gk~~~f~ 74 (76)
.+|.-.+|++|++||.+..|++|-.+
T Consensus 134 ~~l~~~~g~~v~VIItDt~gr~~R~G 159 (245)
T PRK13293 134 EGLEELTGKKVGVIITDTNGRPFRKG 159 (245)
T ss_pred HHHHHHHCCCEEEEEEcCCCcccccC
Confidence 35666789999999999999988665
No 23
>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=43.59 E-value=4.4 Score=20.00 Aligned_cols=12 Identities=42% Similarity=0.933 Sum_probs=8.9
Q ss_pred EEEEcCCCcEEE
Q 038783 61 LIVFSSRGRLYE 72 (76)
Q Consensus 61 liv~~~~gk~~~ 72 (76)
+.+|||+|++|.
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 347899999863
No 24
>COG4831 Roadblock/LC7 domain [Function unknown]
Probab=42.45 E-value=32 Score=22.79 Aligned_cols=30 Identities=33% Similarity=0.329 Sum_probs=23.2
Q ss_pred hhhhhhhccccCceEEEEEEcCCCcEEEccC
Q 038783 45 LKKAYELSVLCDAEVALIVFSSRGRLYEYAN 75 (76)
Q Consensus 45 ~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~s 75 (76)
..|..||.-+-|+-+| =.|+|||++..|-+
T Consensus 2 ~ekLdeLlqi~Gv~AA-Gefs~DGkLv~Ykg 31 (109)
T COG4831 2 SEKLDELLQIKGVMAA-GEFSPDGKLVEYKG 31 (109)
T ss_pred chhHHHHhCccceeEe-ceeCCCCceEEeeC
Confidence 3467888888888554 56899999998854
No 25
>PTZ00033 60S ribosomal protein L24; Provisional
Probab=40.70 E-value=19 Score=24.46 Aligned_cols=27 Identities=7% Similarity=-0.020 Sum_probs=18.9
Q ss_pred hhccccCceE----EEEEEc----CCCcEEEccCC
Q 038783 50 ELSVLCDAEV----ALIVFS----SRGRLYEYANN 76 (76)
Q Consensus 50 ELs~Lcg~~v----~liv~~----~~gk~~~f~s~ 76 (76)
|+|..||..| +...+- .||++|.|+|+
T Consensus 4 ~~C~Fsg~~IyPG~G~~~Vr~~~~~Dgkv~~F~~s 38 (125)
T PTZ00033 4 IACEFSHFAVHPGHGRRYVPFAFLSTKPVLTFLRP 38 (125)
T ss_pred eEecCcCCcccCCCCcEeeecccCCCCCEEEEecH
Confidence 5677777766 334444 78999999874
No 26
>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=39.52 E-value=35 Score=20.47 Aligned_cols=31 Identities=16% Similarity=0.335 Sum_probs=20.4
Q ss_pred hhhhhhhhcccc----CceEEEEEEcCCCcEEEcc
Q 038783 44 LLKKAYELSVLC----DAEVALIVFSSRGRLYEYA 74 (76)
Q Consensus 44 L~KKa~ELs~Lc----g~~v~liv~~~~gk~~~f~ 74 (76)
+++.|.+++... +..|+-+|++++|+....+
T Consensus 7 ~m~~a~~~a~~s~~~~~~~vgaviv~~~~~~i~~g 41 (102)
T PF00383_consen 7 FMRIAIELAKRSRPCGNFPVGAVIVDPDGKIIATG 41 (102)
T ss_dssp HHHHHHHHHHTHBTTTSSSEEEEEEETTTEEEEEE
T ss_pred HHHHHHHHHHhccccCCCCEEEEEEeccCccEEEE
Confidence 455565555544 7789888888777665443
No 27
>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=36.33 E-value=24 Score=28.34 Aligned_cols=26 Identities=23% Similarity=0.512 Sum_probs=19.4
Q ss_pred hccccCceEE---------EEEEcCCCcEEEccCC
Q 038783 51 LSVLCDAEVA---------LIVFSSRGRLYEYANN 76 (76)
Q Consensus 51 Ls~Lcg~~v~---------liv~~~~gk~~~f~s~ 76 (76)
||-.|++.++ ..+..-+|+.|.|||+
T Consensus 382 ~c~vC~~p~~~~~~~~~~~~~~~ey~G~~y~FCS~ 416 (465)
T cd01057 382 LCNVCQVPCVFTEDLTAEAPRVLEYNGRKYHFCSE 416 (465)
T ss_pred CCCCCCCeeccccCcccccceEEEECCEEEEecCH
Confidence 6777888776 3444557999999985
No 28
>PRK09555 feoA ferrous iron transport protein A; Reviewed
Probab=35.87 E-value=75 Score=19.08 Aligned_cols=32 Identities=13% Similarity=0.153 Sum_probs=28.2
Q ss_pred chhhhhhhhhccccCceEEEEEEcCCCcEEEc
Q 038783 42 NGLLKKAYELSVLCDAEVALIVFSSRGRLYEY 73 (76)
Q Consensus 42 ~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f 73 (76)
..+..+..++-++.|++|-++-..|-|.+..|
T Consensus 20 ~~~~~rL~~mGl~pG~~V~v~~~aP~gdPi~i 51 (74)
T PRK09555 20 PAYRQKLLSLGMLPGSSFNVVRVAPLGDPIHI 51 (74)
T ss_pred hHHHHHHHHcCCCCCCEEEEEEECCCCCCEEE
Confidence 45788899999999999999999998887765
No 29
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=32.99 E-value=33 Score=29.32 Aligned_cols=23 Identities=26% Similarity=0.398 Sum_probs=21.1
Q ss_pred ccccCceEEEEEEcCCCcEEEcc
Q 038783 52 SVLCDAEVALIVFSSRGRLYEYA 74 (76)
Q Consensus 52 s~Lcg~~v~liv~~~~gk~~~f~ 74 (76)
++|.|+-++||.++++|.++++.
T Consensus 374 ~VLsgvtaGVi~~d~~g~i~t~N 396 (712)
T COG5000 374 AVLSGLTAGVIGFDNRGCITTVN 396 (712)
T ss_pred HHHhcCceeEEEEcCCCeeEeec
Confidence 69999999999999999999864
No 30
>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=32.31 E-value=59 Score=21.01 Aligned_cols=29 Identities=17% Similarity=0.319 Sum_probs=19.0
Q ss_pred hhhhhhcccc------CceEEEEEEcCCCcEEEcc
Q 038783 46 KKAYELSVLC------DAEVALIVFSSRGRLYEYA 74 (76)
Q Consensus 46 KKa~ELs~Lc------g~~v~liv~~~~gk~~~f~ 74 (76)
+.|-|++-.+ +..|+-||++++|++..-+
T Consensus 2 ~~al~~A~~~~~~~~~~~pvGaviv~~~g~iv~~g 36 (115)
T cd01284 2 RRALELAEKGRGLTSPNPPVGCVIVDDDGEIVGEG 36 (115)
T ss_pred HHHHHHHHhcccccCCCCCEEEEEEeCCCeEEEEe
Confidence 4455555554 6678777777778876644
No 31
>PRK13294 F420-0--gamma-glutamyl ligase; Provisional
Probab=32.27 E-value=33 Score=27.31 Aligned_cols=26 Identities=23% Similarity=0.309 Sum_probs=22.0
Q ss_pred hhhccccCceEEEEEEcCCCcEEEcc
Q 038783 49 YELSVLCDAEVALIVFSSRGRLYEYA 74 (76)
Q Consensus 49 ~ELs~Lcg~~v~liv~~~~gk~~~f~ 74 (76)
.+|.-.+|++|+|||.|..|+++--|
T Consensus 134 ~~l~~~~g~~v~vii~Dt~gr~~r~g 159 (448)
T PRK13294 134 AGLRERLGVDVAVVVTDTMGRAWRNG 159 (448)
T ss_pred HHHHHHHCCCEEEEEecCCCCccccC
Confidence 45777899999999999999987654
No 32
>COG0139 HisI Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]
Probab=31.91 E-value=22 Score=23.75 Aligned_cols=26 Identities=27% Similarity=0.548 Sum_probs=21.2
Q ss_pred hhhhhhhhhccccCceEEEEEEcCCC
Q 038783 43 GLLKKAYELSVLCDAEVALIVFSSRG 68 (76)
Q Consensus 43 GL~KKa~ELs~Lcg~~v~liv~~~~g 68 (76)
|=+-++.|+.+-||.|+.++++.+.|
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 44556789999999999999998755
No 33
>KOG0182 consensus 20S proteasome, regulatory subunit alpha type PSMA6/SCL1 [Posttranslational modification, protein turnover, chaperones]
Probab=31.20 E-value=48 Score=24.86 Aligned_cols=20 Identities=30% Similarity=0.587 Sum_probs=17.3
Q ss_pred cccCceEEEEEEcCCCcEEE
Q 038783 53 VLCDAEVALIVFSSRGRLYE 72 (76)
Q Consensus 53 ~Lcg~~v~liv~~~~gk~~~ 72 (76)
...|-|-.+.||+|.|++|.
T Consensus 5 s~agfDrhitIFspeGrLyQ 24 (246)
T KOG0182|consen 5 SSAGFDRHITIFSPEGRLYQ 24 (246)
T ss_pred CcCCccceEEEECCCceEEe
Confidence 35678999999999999986
No 34
>COG5184 ATS1 Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton]
Probab=30.86 E-value=47 Score=27.16 Aligned_cols=24 Identities=25% Similarity=0.704 Sum_probs=20.2
Q ss_pred hccccCceEEEEEEcCCCcEEEccC
Q 038783 51 LSVLCDAEVALIVFSSRGRLYEYAN 75 (76)
Q Consensus 51 Ls~Lcg~~v~liv~~~~gk~~~f~s 75 (76)
.-+.|+.++.+++.. +|.+|+|++
T Consensus 179 v~l~cg~e~svil~~-~G~V~~~gt 202 (476)
T COG5184 179 VKLACGWEISVILTA-DGRVYSWGT 202 (476)
T ss_pred EEeecCCceEEEEcc-CCcEEEecC
Confidence 457899999888887 579999987
No 35
>PRK09732 hypothetical protein; Provisional
Probab=30.76 E-value=69 Score=21.49 Aligned_cols=29 Identities=17% Similarity=0.173 Sum_probs=21.5
Q ss_pred hhhhhhhccccCceEEEEEEcCCCcEEEc
Q 038783 45 LKKAYELSVLCDAEVALIVFSSRGRLYEY 73 (76)
Q Consensus 45 ~KKa~ELs~Lcg~~v~liv~~~~gk~~~f 73 (76)
..-|.+-+.-=|..|++.|+|.+|.+..|
T Consensus 16 ~~aA~~~A~~~g~~v~iaVvD~~G~l~a~ 44 (134)
T PRK09732 16 IAAGQEEAQKNNWSVSIAVADDGGHLLAL 44 (134)
T ss_pred HHHHHHHHHHhCCCEEEEEEcCCCCEEEE
Confidence 33444445555889999999999998776
No 36
>PF14263 DUF4354: Domain of unknown function (DUF4354); PDB: 3NRF_B 3SB3_A.
Probab=30.25 E-value=18 Score=24.52 Aligned_cols=43 Identities=19% Similarity=0.275 Sum_probs=29.4
Q ss_pred EecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEc
Q 038783 26 RIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEY 73 (76)
Q Consensus 26 ~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f 73 (76)
-+.++.....||.=.-..|..+.-+|+.+ |++.|+++|+-|..
T Consensus 40 sv~~k~~ytktF~V~vaN~s~~~idLsk~-----Cf~a~~~~gk~f~l 82 (124)
T PF14263_consen 40 SVGGKSFYTKTFDVTVANLSDKDIDLSKM-----CFKAYSPDGKEFKL 82 (124)
T ss_dssp EETTEEEEEEEEEEEEEE-SSS-EE-TT------EEEEEETTS-EEEE
T ss_pred eecCccceEEEEEEEEecCCCCccccccc-----hhhhccccCCEEEe
Confidence 34566666777777778888888888888 59999999987653
No 37
>cd01363 Motor_domain Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes.
Probab=30.06 E-value=48 Score=22.44 Aligned_cols=22 Identities=23% Similarity=0.466 Sum_probs=17.2
Q ss_pred ccccCceEEEEEEcCC--CcEEEc
Q 038783 52 SVLCDAEVALIVFSSR--GRLYEY 73 (76)
Q Consensus 52 s~Lcg~~v~liv~~~~--gk~~~f 73 (76)
.++.|-++++++|++. ||.|+-
T Consensus 18 ~~~~G~n~~i~~yG~tGsGKT~Tm 41 (186)
T cd01363 18 SALDGYNVCIFAYGQTGSGKTYTM 41 (186)
T ss_pred HHhCCcceeEEEECCCCCcceEec
Confidence 3467999999999876 777763
No 38
>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=29.61 E-value=8.5 Score=27.84 Aligned_cols=26 Identities=23% Similarity=0.382 Sum_probs=18.7
Q ss_pred hhhccccCceEEEEEEcCCCcEEEcc
Q 038783 49 YELSVLCDAEVALIVFSSRGRLYEYA 74 (76)
Q Consensus 49 ~ELs~Lcg~~v~liv~~~~gk~~~f~ 74 (76)
.+|.-.+|.+|++||.|.+|+++..+
T Consensus 141 ~~l~~~~g~~v~ViI~Dt~gr~~r~G 166 (228)
T PF01996_consen 141 EELKERTGKDVGVIITDTNGRPWRLG 166 (228)
T ss_dssp HHHHHHHS---EEEEEEEEEETTEEC
T ss_pred HHHHHHHCCceEEEEECCCCcEEecC
Confidence 56777899999999999999876655
No 39
>PF02145 Rap_GAP: Rap/ran-GAP; InterPro: IPR000331 The Rap/ran-GAP domain is found in the GTPase activating protein (GAP) responsible for the activation of nuclear Ras-related regulatory proteins Rap1, Rsr1 and Ran in vitro converting it to the putatively inactive GDP-bound state [, ]. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. RanGAP is a leucine rich repeat containing protein which forms a highly curved crescent. Each LRR forms a short beta-strand and a longer alpha-helix that results in a beta-alpha hairpin motif []. The domain is also present in tuberin (a tuberous sclerosis homologue protein) that specifically stimulates the intrinsic GTPase activity of Ras-related protein Rap1A suggesting a possible mechanism for its role in the regulation of cellular growth.; GO: 0005096 GTPase activator activity, 0051056 regulation of small GTPase mediated signal transduction, 0005622 intracellular; PDB: 1SRQ_C 3BRW_B.
Probab=29.56 E-value=28 Score=24.18 Aligned_cols=20 Identities=25% Similarity=0.600 Sum_probs=11.3
Q ss_pred cCceEEEEEEcCCCcEEEcc
Q 038783 55 CDAEVALIVFSSRGRLYEYA 74 (76)
Q Consensus 55 cg~~v~liv~~~~gk~~~f~ 74 (76)
=|.|+++|||.++|..|...
T Consensus 79 IGND~V~IVf~E~~~~y~~~ 98 (188)
T PF02145_consen 79 IGNDIVVIVFNESGQPYDPS 98 (188)
T ss_dssp HTT-SEEEEEESS-----GG
T ss_pred hcCCEEEEEEeCCCCccChh
Confidence 36789999999998887654
No 40
>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=28.60 E-value=24 Score=21.90 Aligned_cols=27 Identities=26% Similarity=0.443 Sum_probs=19.1
Q ss_pred hhhhhhhhhccccCceEEEEEEcCCCc
Q 038783 43 GLLKKAYELSVLCDAEVALIVFSSRGR 69 (76)
Q Consensus 43 GL~KKa~ELs~Lcg~~v~liv~~~~gk 69 (76)
|-+-++.|+.+-||.|.-|+.+.+.|-
T Consensus 37 G~~q~v~~i~~DCD~D~ll~~V~~~G~ 63 (75)
T PF01502_consen 37 GNTQKVVEIRLDCDGDALLFKVEQVGP 63 (75)
T ss_dssp S--EEEEEEEE-TTSSEEEEEEEESS-
T ss_pred CCEEEEEEEEecCCCCeEEEEEEeCCC
Confidence 334556789999999999999877764
No 41
>cd06404 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi,
Probab=27.82 E-value=94 Score=19.68 Aligned_cols=35 Identities=6% Similarity=0.133 Sum_probs=26.9
Q ss_pred hchhhhhhhhhccccCceEEEEEE-cCCCcEEEccC
Q 038783 41 RNGLLKKAYELSVLCDAEVALIVF-SSRGRLYEYAN 75 (76)
Q Consensus 41 k~GL~KKa~ELs~Lcg~~v~liv~-~~~gk~~~f~s 75 (76)
-..|..|+.+++-+-.-+.--+=+ ++.|.+.+++|
T Consensus 22 ~e~L~~~v~~~c~~~~~q~ft~kw~DEEGDp~tiSS 57 (83)
T cd06404 22 LEELCNEVRDMCRFHNDQPFTLKWIDEEGDPCTISS 57 (83)
T ss_pred HHHHHHHHHHHhCCCCCCcEEEEEECCCCCceeecC
Confidence 468999999999887654443434 88999999987
No 42
>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=27.69 E-value=69 Score=22.32 Aligned_cols=19 Identities=16% Similarity=0.632 Sum_probs=15.1
Q ss_pred cccCceEEEEEEcCCCcEE
Q 038783 53 VLCDAEVALIVFSSRGRLY 71 (76)
Q Consensus 53 ~Lcg~~v~liv~~~~gk~~ 71 (76)
.-|++.|-+++|+++-+.|
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 4688899999999988865
No 43
>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=27.46 E-value=33 Score=26.78 Aligned_cols=15 Identities=20% Similarity=0.397 Sum_probs=12.5
Q ss_pred ccccCceEEEEEEcC
Q 038783 52 SVLCDAEVALIVFSS 66 (76)
Q Consensus 52 s~Lcg~~v~liv~~~ 66 (76)
.-+||.+|||+||+.
T Consensus 183 ~~~~~~EICLavYek 197 (334)
T PF06020_consen 183 GQVSGFEICLAVYEK 197 (334)
T ss_pred CccccceEEeeehhh
Confidence 457899999999974
No 44
>cd09011 Glo_EDI_BRP_like_23 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping.
Probab=27.25 E-value=74 Score=19.04 Aligned_cols=18 Identities=6% Similarity=0.182 Sum_probs=14.5
Q ss_pred EEEEEEcCCCcEEEccCC
Q 038783 59 VALIVFSSRGRLYEYANN 76 (76)
Q Consensus 59 v~liv~~~~gk~~~f~s~ 76 (76)
..+.+.+|+|.+..++++
T Consensus 102 r~~~~~DPdGn~iei~~~ 119 (120)
T cd09011 102 RVVRFYDPDKHIIEVGES 119 (120)
T ss_pred EEEEEECCCCCEEEEecc
Confidence 356777999999998875
No 45
>cd01285 nucleoside_deaminase Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia and is a member of the pyrimidine salvage pathway. Cytosine deaminase is found in bacteria and fungi but is not present in mammals; for this reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protei
Probab=27.24 E-value=87 Score=19.48 Aligned_cols=22 Identities=5% Similarity=0.217 Sum_probs=16.2
Q ss_pred ccCceEEEEEEcCCCcEEEccC
Q 038783 54 LCDAEVALIVFSSRGRLYEYAN 75 (76)
Q Consensus 54 Lcg~~v~liv~~~~gk~~~f~s 75 (76)
.-+..|+-+|++++|++...+.
T Consensus 14 ~~~~~vgaviv~~~~~ii~~g~ 35 (109)
T cd01285 14 EGEVPFGAVIVDDDGKVIARGH 35 (109)
T ss_pred cCCCcEEEEEEeCCCEEEEEEe
Confidence 4477888888888888866543
No 46
>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=27.20 E-value=31 Score=19.46 Aligned_cols=22 Identities=27% Similarity=0.603 Sum_probs=17.0
Q ss_pred hhhhhhhhccccCceEEEEEEc
Q 038783 44 LLKKAYELSVLCDAEVALIVFS 65 (76)
Q Consensus 44 L~KKa~ELs~Lcg~~v~liv~~ 65 (76)
|.+.+...+=|||++..|.+|.
T Consensus 2 L~~Rs~~kCELC~a~~~L~vy~ 23 (47)
T smart00782 2 LLARCESKCELCGSDSPLVVYA 23 (47)
T ss_pred hhHHcCCcccCcCCCCCceEEe
Confidence 4556667789999999888883
No 47
>PHA02773 hypothetical protein; Provisional
Probab=26.80 E-value=1.5e+02 Score=19.59 Aligned_cols=35 Identities=20% Similarity=0.513 Sum_probs=25.7
Q ss_pred hhchhhhhhhhhccc-cCceEEEEEEcCCCcEEEcc
Q 038783 40 RRNGLLKKAYELSVL-CDAEVALIVFSSRGRLYEYA 74 (76)
Q Consensus 40 Rk~GL~KKa~ELs~L-cg~~v~liv~~~~gk~~~f~ 74 (76)
..+-|+-.-.|++-. -+-|.|+.+|+..|+++.|-
T Consensus 24 kqkell~rffeiae~de~gdlciply~segdl~lfk 59 (112)
T PHA02773 24 KQKELLIRFFEIAEKDEDGDLCIPLYDSEGDLFLFK 59 (112)
T ss_pred hhHHHHHHHHHHheecCCCCEEEEeecCCCcEEEEe
Confidence 344555666666643 47799999999999998874
No 48
>cd07242 Glo_EDI_BRP_like_6 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=26.33 E-value=66 Score=19.27 Aligned_cols=17 Identities=24% Similarity=0.172 Sum_probs=13.6
Q ss_pred EEEEEcCCCcEEEccCC
Q 038783 60 ALIVFSSRGRLYEYANN 76 (76)
Q Consensus 60 ~liv~~~~gk~~~f~s~ 76 (76)
.+.+++|+|..+.+.+|
T Consensus 112 ~~~~~DpdG~~ie~~~~ 128 (128)
T cd07242 112 ALFFEDPDGIRLELVAP 128 (128)
T ss_pred EEEEECCCCcEEEEEeC
Confidence 45667999999998775
No 49
>cd08356 Glo_EDI_BRP_like_17 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping.
Probab=25.53 E-value=88 Score=18.91 Aligned_cols=17 Identities=12% Similarity=0.335 Sum_probs=14.2
Q ss_pred EEEEEEcCCCcEEEccC
Q 038783 59 VALIVFSSRGRLYEYAN 75 (76)
Q Consensus 59 v~liv~~~~gk~~~f~s 75 (76)
..+.+.||+|.+..++.
T Consensus 97 r~f~~~DPdGn~~~~~~ 113 (113)
T cd08356 97 REFFLHDPSGVLWHIGQ 113 (113)
T ss_pred EEEEEECCCccEEEeeC
Confidence 67888999999988763
No 50
>cd07246 Glo_EDI_BRP_like_8 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The structures of this family demonstrate domain swapping, which is shared by glyoxalase I and antibiotic resistance proteins.
Probab=24.27 E-value=1.2e+02 Score=17.67 Aligned_cols=19 Identities=16% Similarity=-0.073 Sum_probs=15.1
Q ss_pred eEEEEEEcCCCcEEEccCC
Q 038783 58 EVALIVFSSRGRLYEYANN 76 (76)
Q Consensus 58 ~v~liv~~~~gk~~~f~s~ 76 (76)
...+.+.||+|..+.++++
T Consensus 104 ~~~~~~~DP~G~~~~l~~~ 122 (122)
T cd07246 104 DRYGGVRDPFGHRWWIATH 122 (122)
T ss_pred ceEEEEECCCCCEEEEecC
Confidence 4567888999999988764
No 51
>cd08350 BLMT_like BLMT, a bleomycin resistance protein encoded on the transposon Tn5, and similar proteins. BLMT is a bleomycin (Bm) resistance protein, encoded by the ble gene on the transposon Tn5. This protein confers a survival advantage to Escherichia coli host cells. Bm is a glycopeptide antibiotic produced naturally by actinomycetes. It is a potent anti-cancer drug, which acts as a strong DNA-cutting agent, thereby causing cell death. BLMT has strong binding affinity to Bm and it protects against this lethal compound through drug sequestering. BLMT has two identically-folded subdomains, with the same alpha/beta fold; these two halves have no sequence similarity. BLMT is a dimer with two Bm-binding pockets formed at the dimer interface.
Probab=23.64 E-value=96 Score=18.58 Aligned_cols=18 Identities=11% Similarity=0.342 Sum_probs=14.6
Q ss_pred EEEEEEcCCCcEEEccCC
Q 038783 59 VALIVFSSRGRLYEYANN 76 (76)
Q Consensus 59 v~liv~~~~gk~~~f~s~ 76 (76)
..+.+.+|+|....++.+
T Consensus 102 ~~~~~~DPdG~~ie~~~~ 119 (120)
T cd08350 102 REFALVDPDGNLLRFGQP 119 (120)
T ss_pred eEEEEECCCCCEEEeecC
Confidence 467888999999988754
No 52
>PF09816 EAF: RNA polymerase II transcription elongation factor; InterPro: IPR019194 This entry represents the N-terminal domain of ELL-associated factor (Eaf) proteins, which act as transcriptional transactivators of ELL and ELL2 RNA Polymerase II (Pol II) transcriptional elongation factors [, , , ]. Eaf proteins form a stable heterodimer complex with ELL proteins to facilitate the binding of RNA polymerase II to activate transcription elongation. ELL and EAF1 are components of Cajal bodies, which have a role in leukemogenesis []. EAF1 also has the capacity to interact with ELL1 and ELL2. The N terminus of approx 120 of EAF1 has a region of high serine, aspartic acid, and glutamic acid residues [, ].
Probab=23.40 E-value=80 Score=20.05 Aligned_cols=17 Identities=6% Similarity=0.288 Sum_probs=12.7
Q ss_pred CceEEEEEEcCCCcEEE
Q 038783 56 DAEVALIVFSSRGRLYE 72 (76)
Q Consensus 56 g~~v~liv~~~~gk~~~ 72 (76)
...=||+||++..+.|+
T Consensus 76 ~~~ecVLifD~~~~~f~ 92 (109)
T PF09816_consen 76 KEKECVLIFDPETGEFV 92 (109)
T ss_pred CCcEEEEEEECCCCEEE
Confidence 44568999999887654
No 53
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=23.31 E-value=40 Score=27.09 Aligned_cols=45 Identities=22% Similarity=0.316 Sum_probs=37.4
Q ss_pred eEEecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcEEEcc
Q 038783 24 IKRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYA 74 (76)
Q Consensus 24 ik~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~~~f~ 74 (76)
|+.+.|...-..+|.++..| ||+.+|+..+...+++...-+.+|.
T Consensus 18 i~~~~d~~~ps~~~~~~~~~------~~~~~~~g~~~~~~~~~~~~~~~~~ 62 (412)
T COG5068 18 IQGDSDANIPSNTINRLSPG------ELSQQNDGKFDVMIFDSKHSVRVYS 62 (412)
T ss_pred cccccccCCccccccccCcc------cchhhccCCcccccccccccccccC
Confidence 88899999999999999999 9999999988877776655455444
No 54
>COG5184 ATS1 Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton]
Probab=23.16 E-value=91 Score=25.56 Aligned_cols=29 Identities=24% Similarity=0.526 Sum_probs=22.5
Q ss_pred hhhhhccccCceEEEEEEcCCCcEEEccCC
Q 038783 47 KAYELSVLCDAEVALIVFSSRGRLYEYANN 76 (76)
Q Consensus 47 Ka~ELs~Lcg~~v~liv~~~~gk~~~f~s~ 76 (76)
|-..+-+-.|++ .+|+.+.+|++|.|+++
T Consensus 230 ~~~i~qla~G~d-h~i~lt~~G~vy~~Gs~ 258 (476)
T COG5184 230 KKAIVQLAAGAD-HLIALTNEGKVYGWGSN 258 (476)
T ss_pred chheeeeccCCc-eEEEEecCCcEEEecCC
Confidence 344555667778 88888889999999985
No 55
>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=23.11 E-value=61 Score=24.00 Aligned_cols=23 Identities=9% Similarity=0.391 Sum_probs=18.5
Q ss_pred ccccCceEEEEEEcCC--CcEEEcc
Q 038783 52 SVLCDAEVALIVFSSR--GRLYEYA 74 (76)
Q Consensus 52 s~Lcg~~v~liv~~~~--gk~~~f~ 74 (76)
+++-|.++++++|+.+ ||.|+..
T Consensus 68 ~~~~G~n~~i~ayG~tgSGKT~Tm~ 92 (341)
T cd01372 68 GLFEGYNATVLAYGQTGSGKTYTMG 92 (341)
T ss_pred HHhCCCccceeeecCCCCCCcEEec
Confidence 4578999999999764 6888754
No 56
>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=22.88 E-value=1.1e+02 Score=18.62 Aligned_cols=19 Identities=16% Similarity=0.305 Sum_probs=15.1
Q ss_pred ccCceEEEEEEcCCCcEEE
Q 038783 54 LCDAEVALIVFSSRGRLYE 72 (76)
Q Consensus 54 Lcg~~v~liv~~~~gk~~~ 72 (76)
.-|+++|.|.|++....|+
T Consensus 23 ~~G~~~c~V~y~~~t~~F~ 41 (67)
T PF08796_consen 23 KEGVEVCTVTYDQETETFE 41 (67)
T ss_dssp ETTEEEEEEEEETTTTEEE
T ss_pred cCCEEEEEEEEECCCCeEE
Confidence 3588999999988776664
No 57
>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=22.65 E-value=79 Score=23.72 Aligned_cols=22 Identities=18% Similarity=0.409 Sum_probs=17.7
Q ss_pred ccccCceEEEEEEcCC--CcEEEc
Q 038783 52 SVLCDAEVALIVFSSR--GRLYEY 73 (76)
Q Consensus 52 s~Lcg~~v~liv~~~~--gk~~~f 73 (76)
++|-|.+++|++|+.+ ||.|+-
T Consensus 83 ~~l~G~n~~i~ayGqtGSGKT~Tm 106 (356)
T cd01365 83 HAFEGYNVCLFAYGQTGSGKSYTM 106 (356)
T ss_pred HHhCCCceEEEEecCCCCCCeEEe
Confidence 4689999999999765 677763
No 58
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=22.21 E-value=68 Score=19.30 Aligned_cols=27 Identities=7% Similarity=0.156 Sum_probs=17.6
Q ss_pred hhhccccCceEEEEEEcCCCcEEEccC
Q 038783 49 YELSVLCDAEVALIVFSSRGRLYEYAN 75 (76)
Q Consensus 49 ~ELs~Lcg~~v~liv~~~~gk~~~f~s 75 (76)
.+++-||-...+=.|++++..+..||.
T Consensus 16 Aq~A~L~~~g~vdav~s~D~D~llfG~ 42 (73)
T smart00484 16 AQCAYLAKSGLVDAIITEDSDLLLFGA 42 (73)
T ss_pred HHHHHHHhCCCeeEEEcCccceEecCC
Confidence 456666666666666777777776664
No 59
>PF13252 DUF4043: Protein of unknown function (DUF4043)
Probab=21.83 E-value=44 Score=25.79 Aligned_cols=28 Identities=21% Similarity=0.333 Sum_probs=20.9
Q ss_pred hhhhhhccccCceEEEEEEcC--CCcEEEc
Q 038783 46 KKAYELSVLCDAEVALIVFSS--RGRLYEY 73 (76)
Q Consensus 46 KKa~ELs~Lcg~~v~liv~~~--~gk~~~f 73 (76)
..+-.-++|||++++++.|.. +|..|-|
T Consensus 269 ~~~v~ralLlGaQA~~~A~G~~~~~~~~~w 298 (341)
T PF13252_consen 269 NVAVARALLLGAQALVIAFGKSGSGMRFFW 298 (341)
T ss_pred CcceeeeeeechhheeeeeeccCCCccccc
Confidence 345677899999999999966 4455544
No 60
>cd01854 YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.
Probab=21.52 E-value=45 Score=24.39 Aligned_cols=41 Identities=17% Similarity=0.201 Sum_probs=28.8
Q ss_pred EecCCCCcceehhhhhchhhhhhhhhccccCceEEEEEEcCCCcE
Q 038783 26 RIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRL 70 (76)
Q Consensus 26 ~I~n~~~R~~Tf~KRk~GL~KKa~ELs~Lcg~~v~liv~~~~gk~ 70 (76)
.|+.--.|+..+.++..|- + +=.++-++|++++|++.+...
T Consensus 52 ~i~~i~~R~~~l~R~~~~~--~--~~~i~anvD~vllV~d~~~p~ 92 (287)
T cd01854 52 VIVRVLPRKNLLSRPAAGG--R--EQVIAANVDQLVIVVSLNEPF 92 (287)
T ss_pred EEEEEECCCceEEccCCCC--c--ceeEEEeCCEEEEEEEcCCCC
Confidence 3444455777777776662 2 667899999999999876543
No 61
>PF13186 SPASM: Iron-sulfur cluster-binding domain
Probab=21.43 E-value=85 Score=16.72 Aligned_cols=19 Identities=21% Similarity=0.464 Sum_probs=12.7
Q ss_pred cCceEEEEEEcCCCcEEEc
Q 038783 55 CDAEVALIVFSSRGRLYEY 73 (76)
Q Consensus 55 cg~~v~liv~~~~gk~~~f 73 (76)
|++---.+.++++|.+|.-
T Consensus 1 C~~~~~~~~I~~dG~v~pC 19 (64)
T PF13186_consen 1 CGAGWNSLYIDPDGDVYPC 19 (64)
T ss_pred CCCcCeEEEEeeCccEEeC
Confidence 4455556667788988764
No 62
>KOG0712 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=21.36 E-value=1.2e+02 Score=23.74 Aligned_cols=39 Identities=26% Similarity=0.433 Sum_probs=30.6
Q ss_pred ceehhhhhchhhhhhhhhc---cccCceEEEEEEcCCCcEEEccC
Q 038783 34 QVTFCKRRNGLLKKAYELS---VLCDAEVALIVFSSRGRLYEYAN 75 (76)
Q Consensus 34 ~~Tf~KRk~GL~KKa~ELs---~Lcg~~v~liv~~~~gk~~~f~s 75 (76)
...|.+|..+|+.+. .++ -|||-...+- ..+|+.....+
T Consensus 244 h~~F~Rrg~dL~~~~-~i~l~eal~G~~~~~~--~ldGr~l~~~~ 285 (337)
T KOG0712|consen 244 HPGFDRRGSDLYRKL-TISLVEALCGFQRVWE--TLDGRLLKLSS 285 (337)
T ss_pred cccceecccccceee-ecchhhccccceEEEE--ccCCceEEEec
Confidence 888999999999888 888 7899776655 66777665543
No 63
>PF15119 APOC4: Apolipoprotein C4
Probab=21.06 E-value=45 Score=21.77 Aligned_cols=20 Identities=30% Similarity=0.619 Sum_probs=14.9
Q ss_pred hhhhhchhhhhhhhhc--cccC
Q 038783 37 FCKRRNGLLKKAYELS--VLCD 56 (76)
Q Consensus 37 f~KRk~GL~KKa~ELs--~Lcg 56 (76)
...-+..|++|++.|| +|||
T Consensus 75 l~sSkd~llnk~~sLCPrllC~ 96 (99)
T PF15119_consen 75 LRSSKDSLLNKTHSLCPRLLCG 96 (99)
T ss_pred HHHhHHHHHHHHHhhCchhhcc
Confidence 3445788999999887 5665
No 64
>cd01376 KISc_KID_like Kinesin motor domain, KIF22/Kid-like subgroup. Members of this group might play a role in regulating chromosomal movement along microtubules in 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, which repositions the other head domain through
Probab=20.84 E-value=91 Score=23.02 Aligned_cols=22 Identities=14% Similarity=0.351 Sum_probs=17.5
Q ss_pred ccccCceEEEEEEcCC--CcEEEc
Q 038783 52 SVLCDAEVALIVFSSR--GRLYEY 73 (76)
Q Consensus 52 s~Lcg~~v~liv~~~~--gk~~~f 73 (76)
+++-|.++++++|+.+ ||.|+.
T Consensus 75 ~~~~G~n~~i~ayG~tgSGKTyTm 98 (319)
T cd01376 75 HLLSGQNATVFAYGSTGAGKTHTM 98 (319)
T ss_pred HHhCCCceEEEEECCCCCCCcEEE
Confidence 4567999999999765 687764
No 65
>PF04873 EIN3: Ethylene insensitive 3; InterPro: IPR006957 Ethylene insensitive 3 (EIN3) proteins are a family of plant DNA-binding proteins that regulate transcription in response to the gaseous plant hormone ethylene, and are essential for ethylene-mediated responses. In the presence of ethylene, dark-grown dicotyledonous seedlings undergo dramatic morphological changes collectively known as the 'triple response'. In Arabidopsis, these changes consist of a radial swelling of the hypocotyl, an exaggeration in the curvature of the apical hook, and the inhibition of cell elongation in the hypocotyl and root.; GO: 0005634 nucleus; PDB: 1WIJ_A.
Probab=20.62 E-value=33 Score=26.76 Aligned_cols=38 Identities=26% Similarity=0.415 Sum_probs=0.0
Q ss_pred hhhchhhhhhhhhccccCceEEE-EEEcCCCcEEEccCC
Q 038783 39 KRRNGLLKKAYELSVLCDAEVAL-IVFSSRGRLYEYANN 76 (76)
Q Consensus 39 KRk~GL~KKa~ELs~Lcg~~v~l-iv~~~~gk~~~f~s~ 76 (76)
.=..|++|=+.-..-||+|.-++ -+++..|++.+|+|+
T Consensus 51 ~aqd~ilkym~~~m~~~n~~gfvy~~~~~~~k~~~~~s~ 89 (354)
T PF04873_consen 51 RAQDGILKYMFPEMELCNAPGFVYTIISSSGKPVEGVSP 89 (354)
T ss_dssp ---------------------------------------
T ss_pred hhhhHHHHhhccccccccCceeeecCCCCCCCccCCcCC
Confidence 33467777777778999999998 788889999999875
No 66
>cd07261 Glo_EDI_BRP_like_11 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping.
Probab=20.10 E-value=1.2e+02 Score=17.67 Aligned_cols=16 Identities=6% Similarity=0.212 Sum_probs=12.6
Q ss_pred EEEEEcCCCcEEEccC
Q 038783 60 ALIVFSSRGRLYEYAN 75 (76)
Q Consensus 60 ~liv~~~~gk~~~f~s 75 (76)
.+.+.+|+|..+.+.+
T Consensus 99 ~~~~~DPdGn~ie~~~ 114 (114)
T cd07261 99 TFVALDPDGHRLRVFA 114 (114)
T ss_pred EEEEECCCCCEEEeeC
Confidence 4678899999887754
Done!