Query 035470
Match_columns 62
No_of_seqs 112 out of 962
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 03:11:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035470.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035470hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0014 MADS box transcription 100.0 3.8E-32 8.3E-37 175.3 2.9 61 1-61 1-61 (195)
2 cd00265 MADS_MEF2_like MEF2 (m 100.0 9.2E-32 2E-36 156.8 3.7 61 2-62 1-61 (77)
3 smart00432 MADS MADS domain. 100.0 2.2E-31 4.7E-36 149.3 4.5 59 2-60 1-59 (59)
4 cd00120 MADS MADS: MCM1, Agamo 100.0 3E-30 6.5E-35 144.6 4.0 59 2-60 1-59 (59)
5 cd00266 MADS_SRF_like SRF-like 100.0 2.2E-29 4.8E-34 148.4 3.2 60 2-61 1-60 (83)
6 PF00319 SRF-TF: SRF-type tran 99.9 7.9E-29 1.7E-33 135.6 0.2 51 9-59 1-51 (51)
7 KOG0015 Regulator of arginine 99.9 1.1E-22 2.4E-27 143.1 3.4 60 2-61 63-122 (338)
8 COG5068 ARG80 Regulator of arg 99.7 5.7E-17 1.2E-21 117.3 3.8 61 1-61 81-141 (412)
9 PF09151 DUF1936: Domain of un 70.9 5.3 0.00012 20.0 2.2 24 34-57 2-25 (36)
10 PRK00807 50S ribosomal protein 69.0 6.7 0.00014 21.0 2.5 27 34-60 2-32 (52)
11 PRK14891 50S ribosomal protein 68.4 3.9 8.4E-05 26.2 1.7 27 34-60 5-35 (131)
12 cd00472 Ribosomal_L24e_L24 Rib 66.0 6.4 0.00014 21.4 2.1 27 34-60 4-34 (54)
13 PF13540 RCC1_2: Regulator of 63.7 13 0.00028 17.3 2.7 25 36-61 3-27 (30)
14 PF01246 Ribosomal_L24e: Ribos 60.2 8.6 0.00019 22.0 2.0 27 34-60 4-34 (71)
15 TIGR01916 F420_cofE F420-0:gam 59.8 6.4 0.00014 27.4 1.7 28 34-61 134-161 (243)
16 PF04945 YHS: YHS domain; Int 56.7 10 0.00022 19.3 1.7 22 39-60 6-30 (47)
17 PF09941 DUF2173: Uncharacteri 54.3 16 0.00035 22.6 2.6 28 31-59 2-29 (108)
18 PF07676 PD40: WD40-like Beta 54.1 13 0.00027 17.6 1.8 19 42-60 10-28 (39)
19 COG4831 Roadblock/LC7 domain [ 53.4 16 0.00035 22.6 2.5 31 29-60 2-32 (109)
20 PF10584 Proteasome_A_N: Prote 51.1 3 6.5E-05 19.2 -0.8 11 46-56 6-16 (23)
21 PTZ00033 60S ribosomal protein 51.1 12 0.00026 23.8 1.7 27 34-60 4-38 (125)
22 KOG0183 20S proteasome, regula 49.2 14 0.0003 25.9 1.9 17 40-56 3-19 (249)
23 PRK13293 F420-0--gamma-glutamy 48.6 12 0.00026 26.1 1.6 28 34-61 135-162 (245)
24 COG2075 RPL24A Ribosomal prote 46.9 23 0.00049 20.2 2.3 26 35-60 5-34 (66)
25 KOG0184 20S proteasome, regula 44.9 14 0.00029 26.0 1.3 21 36-56 3-23 (254)
26 PRK09555 feoA ferrous iron tra 42.3 53 0.0012 18.5 3.4 33 26-58 20-52 (74)
27 PF14263 DUF4354: Domain of un 38.8 17 0.00038 22.9 1.1 42 11-57 41-82 (124)
28 PF01502 PRA-CH: Phosphoribosy 38.2 17 0.00036 21.1 0.9 33 21-53 22-63 (75)
29 cd01057 AAMH_A Aromatic and Al 38.2 22 0.00048 26.7 1.7 26 35-60 382-416 (465)
30 COG0139 HisI Phosphoribosyl-AM 37.4 18 0.00039 22.6 0.9 25 28-52 70-94 (111)
31 PF11232 Med25: Mediator compl 37.0 41 0.00089 21.9 2.6 19 37-55 109-127 (152)
32 PHA02773 hypothetical protein; 36.4 90 0.0019 19.2 3.9 47 15-61 15-62 (112)
33 PRK13294 F420-0--gamma-glutamy 36.3 24 0.00051 26.3 1.6 28 34-61 135-162 (448)
34 PF04873 EIN3: Ethylene insens 36.1 12 0.00026 27.3 0.0 38 25-62 53-91 (354)
35 COG5000 NtrY Signal transducti 35.4 29 0.00062 27.7 2.0 23 36-58 374-396 (712)
36 PF12860 PAS_7: PAS fold 34.2 47 0.001 18.8 2.4 19 41-59 4-22 (115)
37 cd07242 Glo_EDI_BRP_like_6 Thi 33.9 47 0.001 18.8 2.3 17 44-60 112-128 (128)
38 cd01854 YjeQ_engC YjeQ/EngC. 33.1 31 0.00067 23.7 1.7 41 10-54 52-92 (287)
39 PF09943 DUF2175: Uncharacteri 32.4 49 0.0011 20.3 2.3 20 36-61 5-24 (101)
40 PF01996 F420_ligase: F420-0:G 32.3 4 8.7E-05 27.7 -2.8 29 33-61 141-169 (228)
41 KOG0182 20S proteasome, regula 31.9 45 0.00098 23.4 2.3 19 38-56 6-24 (246)
42 PF00383 dCMP_cyt_deam_1: Cyti 31.6 49 0.0011 18.6 2.1 30 28-57 7-40 (102)
43 KOG0641 WD40 repeat protein [G 31.4 61 0.0013 23.3 2.9 33 29-61 19-53 (350)
44 cd09011 Glo_EDI_BRP_like_23 Th 30.6 70 0.0015 18.0 2.7 17 44-60 103-119 (120)
45 COG5068 ARG80 Regulator of arg 30.1 25 0.00055 26.4 0.8 46 8-59 18-63 (412)
46 PF13082 DUF3931: Protein of u 29.6 29 0.00062 19.3 0.8 37 4-40 6-44 (66)
47 cd08350 BLMT_like BLMT, a bleo 28.0 82 0.0018 17.8 2.7 18 43-60 102-119 (120)
48 PF01849 NAC: NAC domain; Int 26.7 37 0.0008 18.1 0.9 18 45-62 22-39 (58)
49 KOG0278 Serine/threonine kinas 26.6 77 0.0017 23.0 2.8 19 43-61 270-288 (334)
50 cd06404 PB1_aPKC PB1 domain is 26.4 76 0.0016 18.8 2.3 36 25-60 22-58 (83)
51 cd01284 Riboflavin_deaminase-r 26.4 89 0.0019 18.9 2.7 28 30-57 2-35 (115)
52 KOG0712 Molecular chaperone (D 25.8 1.1E+02 0.0025 22.3 3.6 40 18-60 244-286 (337)
53 smart00782 PhnA_Zn_Ribbon PhnA 25.7 32 0.0007 18.1 0.6 22 28-49 2-23 (47)
54 cd06397 PB1_UP1 Uncharacterize 25.0 86 0.0019 18.6 2.4 36 25-60 22-57 (82)
55 PF09695 YtfJ_HI0045: Bacteria 25.0 75 0.0016 20.9 2.3 36 19-57 105-140 (160)
56 COG4888 Uncharacterized Zn rib 24.4 1.5E+02 0.0033 18.3 3.4 55 1-58 1-59 (104)
57 cd07264 Glo_EDI_BRP_like_15 Th 24.3 98 0.0021 17.2 2.5 16 45-60 110-125 (125)
58 COG1918 FeoA Fe2+ transport sy 24.0 1.5E+02 0.0033 16.8 3.2 31 26-56 21-51 (75)
59 cd01372 KISc_KIF4 Kinesin moto 23.3 64 0.0014 22.4 1.9 25 36-60 68-94 (341)
60 cd01363 Motor_domain Myosin an 23.1 73 0.0016 20.2 2.0 21 37-57 19-41 (186)
61 cd08356 Glo_EDI_BRP_like_17 Th 22.8 1.2E+02 0.0026 17.2 2.7 17 43-59 97-113 (113)
62 cd07246 Glo_EDI_BRP_like_8 Thi 22.7 1.5E+02 0.0032 16.3 3.2 19 42-60 104-122 (122)
63 cd07244 FosA FosA, a Fosfomyci 22.6 1.1E+02 0.0023 17.4 2.5 18 44-61 94-111 (121)
64 PF13186 SPASM: Iron-sulfur cl 22.3 81 0.0018 15.8 1.8 19 39-57 1-19 (64)
65 PF09729 Gti1_Pac2: Gti1/Pac2 22.2 53 0.0012 21.7 1.2 30 20-49 137-166 (168)
66 cd01365 KISc_KIF1A_KIF1B Kines 22.2 79 0.0017 22.3 2.2 22 36-57 83-106 (356)
67 PRK09732 hypothetical protein; 22.2 1.1E+02 0.0024 19.2 2.6 28 31-58 18-45 (134)
68 PF14009 DUF4228: Domain of un 21.9 1.1E+02 0.0025 18.5 2.6 22 39-60 12-33 (181)
69 PF08796 DUF1797: Protein of u 21.3 1.4E+02 0.003 17.0 2.7 18 39-56 24-41 (67)
70 PF09158 MotCF: Bacteriophage 21.1 43 0.00093 20.6 0.6 24 5-28 19-43 (103)
71 PHA02757 hypothetical protein; 20.9 1.3E+02 0.0029 17.3 2.5 18 42-59 46-64 (75)
72 cd03750 proteasome_alpha_type_ 20.7 26 0.00057 23.1 -0.5 13 44-56 4-16 (227)
73 COG0529 CysC Adenylylsulfate k 20.3 45 0.00098 22.7 0.6 25 19-43 133-159 (197)
74 PF03989 DNA_gyraseA_C: DNA gy 20.0 86 0.0019 15.4 1.5 16 45-60 3-18 (48)
No 1
>KOG0014 consensus MADS box transcription factor [Transcription]
Probab=99.97 E-value=3.8e-32 Score=175.33 Aligned_cols=61 Identities=66% Similarity=1.103 Sum_probs=60.2
Q ss_pred CCccceeeEEeccccCcceehhhccchhhhhhhhcceecCceEEEEEEcCCCCeEEecCCC
Q 035470 1 MGRGRVQLKRIENKINRQVTFSKRRSGLLKKAHEISVLCDAEVALIVFSTKGKLFEYSTDS 61 (62)
Q Consensus 1 mgR~ki~ik~I~~~~~R~~tf~KR~~GL~KKa~ELs~Lc~~~v~~iv~~~~g~~~~~~s~~ 61 (62)
|||+||+|++|+|+..|++||+||+.||||||+||||||||+||+|||+|+|++|.|++++
T Consensus 1 M~R~ki~i~~Ien~~~RqvTFsKRr~GL~KKA~ELsvLCd~eiavIifsp~~~~~~~~~~~ 61 (195)
T KOG0014|consen 1 MGRGKIEIKRIENESSRQVTFSKRRNGLFKKASELSVLCDAEIAVIVFSPSGKLYEFGSSD 61 (195)
T ss_pred CCCCccceeeccccchhhhhhHHHHhhHHHHHHHHHHhcCCeEEEEEECCCCCccccCCcc
Confidence 9999999999999999999999999999999999999999999999999999999999986
No 2
>cd00265 MADS_MEF2_like MEF2 (myocyte enhancer factor 2)-like/Type II subfamily of MADS ( MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero and homo-dimers. Differs from SRF-like/Type I subgroup mainly in position of the alpha helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=99.97 E-value=9.2e-32 Score=156.78 Aligned_cols=61 Identities=74% Similarity=1.167 Sum_probs=59.7
Q ss_pred CccceeeEEeccccCcceehhhccchhhhhhhhcceecCceEEEEEEcCCCCeEEecCCCC
Q 035470 2 GRGRVQLKRIENKINRQVTFSKRRSGLLKKAHEISVLCDAEVALIVFSTKGKLFEYSTDSW 62 (62)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KR~~GL~KKa~ELs~Lc~~~v~~iv~~~~g~~~~~~s~~~ 62 (62)
||+||+|++|+|+.+|++||+||+.||||||.|||+||||+||+++|+|+|++|+|+||++
T Consensus 1 gr~ki~i~~i~~~~~r~~tf~kR~~gl~kKa~Els~Lc~~~v~lvv~sp~gk~~~f~s~s~ 61 (77)
T cd00265 1 GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSPSM 61 (77)
T ss_pred CCCcceeEEecCccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCCCceEEecCCCH
Confidence 8999999999999999999999999999999999999999999999999999999999974
No 3
>smart00432 MADS MADS domain.
Probab=99.97 E-value=2.2e-31 Score=149.27 Aligned_cols=59 Identities=73% Similarity=1.151 Sum_probs=58.2
Q ss_pred CccceeeEEeccccCcceehhhccchhhhhhhhcceecCceEEEEEEcCCCCeEEecCC
Q 035470 2 GRGRVQLKRIENKINRQVTFSKRRSGLLKKAHEISVLCDAEVALIVFSTKGKLFEYSTD 60 (62)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KR~~GL~KKa~ELs~Lc~~~v~~iv~~~~g~~~~~~s~ 60 (62)
||+||+|++|+|+..|++||+||+.||+|||+|||+|||++||+|+|+|+|++++|++|
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
>cd00120 MADS MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators. Binds DNA and exists as hetero and homo-dimers. Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ Type II. These subgroups differ mainly in position of the alpha 2 helix responsible for the dimerization interface; Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=99.96 E-value=3e-30 Score=144.60 Aligned_cols=59 Identities=69% Similarity=1.112 Sum_probs=57.9
Q ss_pred CccceeeEEeccccCcceehhhccchhhhhhhhcceecCceEEEEEEcCCCCeEEecCC
Q 035470 2 GRGRVQLKRIENKINRQVTFSKRRSGLLKKAHEISVLCDAEVALIVFSTKGKLFEYSTD 60 (62)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KR~~GL~KKa~ELs~Lc~~~v~~iv~~~~g~~~~~~s~ 60 (62)
||+||+|++|+|+..|++||+||+.||+|||+|||+|||++||+|+|+|+|++++|++|
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 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=99.95 E-value=2.2e-29 Score=148.35 Aligned_cols=60 Identities=60% Similarity=0.940 Sum_probs=58.7
Q ss_pred CccceeeEEeccccCcceehhhccchhhhhhhhcceecCceEEEEEEcCCCCeEEecCCC
Q 035470 2 GRGRVQLKRIENKINRQVTFSKRRSGLLKKAHEISVLCDAEVALIVFSTKGKLFEYSTDS 61 (62)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KR~~GL~KKa~ELs~Lc~~~v~~iv~~~~g~~~~~~s~~ 61 (62)
||+||+|++|+|+.+|++||+||+.||+|||+|||+|||++||+|+|+|+|+.+.|.+++
T Consensus 1 gr~Ki~i~~I~~~~~R~~tf~KRk~gl~kKa~ELs~Lc~~~v~~iv~sp~~~~~~~~~~~ 60 (83)
T cd00266 1 GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPSS 60 (83)
T ss_pred CCccceeEEeeccchhhhhHHHhhhhHHHHHHHHHHhhCCcEEEEEECCCCCcceecCcH
Confidence 799999999999999999999999999999999999999999999999999999999875
No 6
>PF00319 SRF-TF: SRF-type transcription factor (DNA-binding and dimerisation domain); InterPro: IPR002100 Human serum response factor (SRF) is a ubiquitous nuclear protein important for cell proliferation and differentiation. SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as c-fos oncogene and muscle-specific actin genes. A core domain of around 90 amino acids is sufficient for the activities of DNA-binding, dimerisation and interaction with accessory factors. Within the core is a DNA-binding region, designated the MADS box [], that is highly similar to many eukaryotic regulatory proteins: among these are MCM1, the regulator of cell type-specific genes in fission yeast; DSRF, a Drosophila trachea development factor; the MEF2 family of myocyte-specific enhancer factors; and the Agamous and Deficiens families of plant homeotic proteins. In SRF, the MADS box has been shown to be involved in DNA-binding and dimerisation []. Proteins belonging to the MADS family function as dimers, the primary DNA-binding element of which is an anti-parallel coiled coil of two amphipathic alpha-helices, one from each subunit. The DNA wraps around the coiled coil allowing the basic N-termini of the helices to fit into the DNA major groove. The chain extending from the helix N-termini reaches over the DNA backbone and penetrates into the minor groove. A 4-stranded, anti-parallel beta-sheet packs against the coiled-coil face opposite the DNA and is the central element of the dimerisation interface. The MADS-box domain is commonly found associated with K-box region see IPR002487 from INTERPRO ; GO: 0003677 DNA binding, 0046983 protein dimerization activity; PDB: 1MNM_B 1N6J_A 1TQE_S 3MU6_D 3P57_I 1EGW_A 1C7U_B 3KOV_A 1HBX_A 1K6O_C ....
Probab=99.94 E-value=7.9e-29 Score=135.63 Aligned_cols=51 Identities=63% Similarity=1.006 Sum_probs=47.0
Q ss_pred EEeccccCcceehhhccchhhhhhhhcceecCceEEEEEEcCCCCeEEecC
Q 035470 9 KRIENKINRQVTFSKRRSGLLKKAHEISVLCDAEVALIVFSTKGKLFEYST 59 (62)
Q Consensus 9 k~I~~~~~R~~tf~KR~~GL~KKa~ELs~Lc~~~v~~iv~~~~g~~~~~~s 59 (62)
++|+|+..|++||+||++||+|||+|||+|||++||+|+|+|+|++|+|+|
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=99.86 E-value=1.1e-22 Score=143.12 Aligned_cols=60 Identities=43% Similarity=0.739 Sum_probs=58.7
Q ss_pred CccceeeEEeccccCcceehhhccchhhhhhhhcceecCceEEEEEEcCCCCeEEecCCC
Q 035470 2 GRGRVQLKRIENKINRQVTFSKRRSGLLKKAHEISVLCDAEVALIVFSTKGKLFEYSTDS 61 (62)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KR~~GL~KKa~ELs~Lc~~~v~~iv~~~~g~~~~~~s~~ 61 (62)
||+||+|+||+|+..|.+||+|||.||||||+||++|+|.+|-|+|.+++|.+|+|++|-
T Consensus 63 gr~kik~eyIenK~rR~~tFSKRK~GImKKAyELs~LTGtqVllLVaSEtGhVyTFaTpK 122 (338)
T KOG0015|consen 63 GRVKIKMEYIENKLRRYVTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATPK 122 (338)
T ss_pred ceeeccchhhcccceeeeeehhhhhhhHHHHHHhhhcccceEEEEEEecCcceEEecccc
Confidence 799999999999999999999999999999999999999999999999999999999984
No 8
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.66 E-value=5.7e-17 Score=117.34 Aligned_cols=61 Identities=41% Similarity=0.611 Sum_probs=60.0
Q ss_pred CCccceeeEEeccccCcceehhhccchhhhhhhhcceecCceEEEEEEcCCCCeEEecCCC
Q 035470 1 MGRGRVQLKRIENKINRQVTFSKRRSGLLKKAHEISVLCDAEVALIVFSTKGKLFEYSTDS 61 (62)
Q Consensus 1 mgR~ki~ik~I~~~~~R~~tf~KR~~GL~KKa~ELs~Lc~~~v~~iv~~~~g~~~~~~s~~ 61 (62)
||++++.|.+|+|+.+|.+||.||+.||+|||+||++|+|.+|.+++.+++|.+|+|++|+
T Consensus 81 ~~~~~~~is~i~nk~~r~vtf~Krk~gI~kka~ElsvLt~~~vl~lvise~g~v~tf~tp~ 141 (412)
T COG5068 81 VTGRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTTPK 141 (412)
T ss_pred cccccCCcccccCcccccchhhhhhhhhhhhhhhhhhccCCceEEEEecCCCceeeecCCc
Confidence 7899999999999999999999999999999999999999999999999999999999986
No 9
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=70.94 E-value=5.3 Score=19.99 Aligned_cols=24 Identities=21% Similarity=0.421 Sum_probs=17.1
Q ss_pred hcceecCceEEEEEEcCCCCeEEe
Q 035470 34 EISVLCDAEVALIVFSTKGKLFEY 57 (62)
Q Consensus 34 ELs~Lc~~~v~~iv~~~~g~~~~~ 57 (62)
.|+--||+-|.+.+|+..|.+-.|
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 366679999999999999976655
No 10
>PRK00807 50S ribosomal protein L24e; Validated
Probab=68.99 E-value=6.7 Score=21.03 Aligned_cols=27 Identities=11% Similarity=0.432 Sum_probs=19.6
Q ss_pred hcceecCceEE----EEEEcCCCCeEEecCC
Q 035470 34 EISVLCDAEVA----LIVFSTKGKLFEYSTD 60 (62)
Q Consensus 34 ELs~Lc~~~v~----~iv~~~~g~~~~~~s~ 60 (62)
+++..||-+|. ...+..+|++|.|+|+
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~Fcs~ 32 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILYFCSS 32 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEEEeCH
Confidence 45667777775 4445678999999985
No 11
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=68.44 E-value=3.9 Score=26.22 Aligned_cols=27 Identities=7% Similarity=0.262 Sum_probs=21.2
Q ss_pred hcceecCceE----EEEEEcCCCCeEEecCC
Q 035470 34 EISVLCDAEV----ALIVFSTKGKLFEYSTD 60 (62)
Q Consensus 34 ELs~Lc~~~v----~~iv~~~~g~~~~~~s~ 60 (62)
++|..||.+| ..+.+..+|++|.|+|+
T Consensus 5 e~CsFcG~kIyPG~G~~fVR~DGkvf~Fcss 35 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMFVRKDGTVLHFVDS 35 (131)
T ss_pred eeecCcCCcccCCCCcEEEecCCCEEEEecH
Confidence 5778888887 34555778999999985
No 12
>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=65.96 E-value=6.4 Score=21.42 Aligned_cols=27 Identities=19% Similarity=0.534 Sum_probs=19.9
Q ss_pred hcceecCceE----EEEEEcCCCCeEEecCC
Q 035470 34 EISVLCDAEV----ALIVFSTKGKLFEYSTD 60 (62)
Q Consensus 34 ELs~Lc~~~v----~~iv~~~~g~~~~~~s~ 60 (62)
|+|..||-+| ....+..||+++.|+|.
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 6677788777 34445678999999985
No 13
>PF13540 RCC1_2: Regulator of chromosome condensation (RCC1) repeat; PDB: 3QI0_D 1JTD_B 3QHY_B.
Probab=63.68 E-value=13 Score=17.28 Aligned_cols=25 Identities=12% Similarity=0.393 Sum_probs=16.6
Q ss_pred ceecCceEEEEEEcCCCCeEEecCCC
Q 035470 36 SVLCDAEVALIVFSTKGKLFEYSTDS 61 (62)
Q Consensus 36 s~Lc~~~v~~iv~~~~g~~~~~~s~~ 61 (62)
++-||..-.+.+.+ +|.+|.|++.+
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 45677777666665 69999998764
No 14
>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=60.15 E-value=8.6 Score=22.02 Aligned_cols=27 Identities=15% Similarity=0.356 Sum_probs=17.1
Q ss_pred hcceecCceE----EEEEEcCCCCeEEecCC
Q 035470 34 EISVLCDAEV----ALIVFSTKGKLFEYSTD 60 (62)
Q Consensus 34 ELs~Lc~~~v----~~iv~~~~g~~~~~~s~ 60 (62)
|+|..||-+| ..+.+..||+++.|+|.
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 5677788777 34555789999999874
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=59.83 E-value=6.4 Score=27.39 Aligned_cols=28 Identities=21% Similarity=0.362 Sum_probs=23.8
Q ss_pred hcceecCceEEEEEEcCCCCeEEecCCC
Q 035470 34 EISVLCDAEVALIVFSTKGKLFEYSTDS 61 (62)
Q Consensus 34 ELs~Lc~~~v~~iv~~~~g~~~~~~s~~ 61 (62)
+|.-.+|++|++||.+..|..+.-++.+
T Consensus 134 ~l~~~~g~~v~VIItDt~gr~~R~G~~g 161 (243)
T TIGR01916 134 GLRELTGVDVGVIITDTNGRPFREGQVG 161 (243)
T ss_pred HHHHHHCCCEEEEEECCCCCccccCCCC
Confidence 4666799999999999999999877765
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=56.67 E-value=10 Score=19.29 Aligned_cols=22 Identities=18% Similarity=0.516 Sum_probs=14.0
Q ss_pred cCceE---EEEEEcCCCCeEEecCC
Q 035470 39 CDAEV---ALIVFSTKGKLFEYSTD 60 (62)
Q Consensus 39 c~~~v---~~iv~~~~g~~~~~~s~ 60 (62)
||..| +-.-..-+|+.|-|+|.
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 55555 44455568999999985
No 17
>PF09941 DUF2173: Uncharacterized conserved protein (DUF2173); InterPro: IPR018685 This family of various hypothetical prokaryotic proteins has no known function.
Probab=54.28 E-value=16 Score=22.55 Aligned_cols=28 Identities=36% Similarity=0.374 Sum_probs=21.4
Q ss_pred hhhhcceecCceEEEEEEcCCCCeEEecC
Q 035470 31 KAHEISVLCDAEVALIVFSTKGKLFEYST 59 (62)
Q Consensus 31 Ka~ELs~Lc~~~v~~iv~~~~g~~~~~~s 59 (62)
+..||..|.||- |...|+++|++..|-.
T Consensus 2 ~l~~Lm~lpGv~-AAg~Fs~~G~l~e~~G 29 (108)
T PF09941_consen 2 KLDKLMKLPGVV-AAGEFSDDGKLVEYKG 29 (108)
T ss_pred cHHHhhcCCCeE-EEEEECCCCeEEeeec
Confidence 346788888885 5578999999998854
No 18
>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=54.08 E-value=13 Score=17.64 Aligned_cols=19 Identities=16% Similarity=0.361 Sum_probs=13.9
Q ss_pred eEEEEEEcCCCCeEEecCC
Q 035470 42 EVALIVFSTKGKLFEYSTD 60 (62)
Q Consensus 42 ~v~~iv~~~~g~~~~~~s~ 60 (62)
.-.-..++|+|+...|+|.
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 3456788999999999873
No 19
>COG4831 Roadblock/LC7 domain [Function unknown]
Probab=53.43 E-value=16 Score=22.60 Aligned_cols=31 Identities=32% Similarity=0.365 Sum_probs=23.8
Q ss_pred hhhhhhcceecCceEEEEEEcCCCCeEEecCC
Q 035470 29 LKKAHEISVLCDAEVALIVFSTKGKLFEYSTD 60 (62)
Q Consensus 29 ~KKa~ELs~Lc~~~v~~iv~~~~g~~~~~~s~ 60 (62)
+.|..||.-+-|+-+ .=.|+|+|++..|-++
T Consensus 2 ~ekLdeLlqi~Gv~A-AGefs~DGkLv~Ykgd 32 (109)
T COG4831 2 SEKLDELLQIKGVMA-AGEFSPDGKLVEYKGD 32 (109)
T ss_pred chhHHHHhCccceeE-eceeCCCCceEEeeCC
Confidence 346778888888754 4678999999999765
No 20
>PF10584 Proteasome_A_N: Proteasome subunit A N-terminal signature; InterPro: IPR000426 The proteasome (or macropain) (3.4.25.1 from EC) [, , , , ] is a eukaryotic and archaeal multicatalytic proteinase complex that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. In eukaryotes the proteasome is composed of about 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700 kDa. Most proteasome subunits can be classified, on the basis on sequence similarities into two groups, alpha (A) and beta (B). This family contains the alpha subunit sequences which range from 210 to 290 amino acids. These sequences are classified as non-peptidase homologues in MEROPS peptidase family T1 (clan PB(T)). ; GO: 0004175 endopeptidase activity, 0006511 ubiquitin-dependent protein catabolic process, 0019773 proteasome core complex, alpha-subunit complex; PDB: 3H4P_M 1IRU_O 3UN4_U 1FNT_A 3OEV_G 3OEU_U 3SDK_U 3DY3_G 3MG7_G 3L5Q_C ....
Probab=51.12 E-value=3 Score=19.21 Aligned_cols=11 Identities=45% Similarity=0.945 Sum_probs=8.4
Q ss_pred EEEcCCCCeEE
Q 035470 46 IVFSTKGKLFE 56 (62)
Q Consensus 46 iv~~~~g~~~~ 56 (62)
.+|||+|++|+
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 46899998863
No 21
>PTZ00033 60S ribosomal protein L24; Provisional
Probab=51.10 E-value=12 Score=23.79 Aligned_cols=27 Identities=4% Similarity=-0.006 Sum_probs=18.9
Q ss_pred hcceecCceE----EEEEEc----CCCCeEEecCC
Q 035470 34 EISVLCDAEV----ALIVFS----TKGKLFEYSTD 60 (62)
Q Consensus 34 ELs~Lc~~~v----~~iv~~----~~g~~~~~~s~ 60 (62)
|+|..||..| ....+. .||++|.|+|+
T Consensus 4 ~~C~Fsg~~IyPG~G~~~Vr~~~~~Dgkv~~F~~s 38 (125)
T PTZ00033 4 IACEFSHFAVHPGHGRRYVPFAFLSTKPVLTFLRP 38 (125)
T ss_pred eEecCcCCcccCCCCcEeeecccCCCCCEEEEecH
Confidence 5666777766 233444 89999999985
No 22
>KOG0183 consensus 20S proteasome, regulatory subunit alpha type PSMA7/PRE6 [Posttranslational modification, protein turnover, chaperones]
Probab=49.24 E-value=14 Score=25.87 Aligned_cols=17 Identities=47% Similarity=0.727 Sum_probs=14.3
Q ss_pred CceEEEEEEcCCCCeEE
Q 035470 40 DAEVALIVFSTKGKLFE 56 (62)
Q Consensus 40 ~~~v~~iv~~~~g~~~~ 56 (62)
+-|-|+-||||+|.+++
T Consensus 3 rydraltvFSPDGhL~Q 19 (249)
T KOG0183|consen 3 RYDRALTVFSPDGHLFQ 19 (249)
T ss_pred ccccceEEECCCCCEEe
Confidence 34678999999999986
No 23
>PRK13293 F420-0--gamma-glutamyl ligase; Reviewed
Probab=48.63 E-value=12 Score=26.07 Aligned_cols=28 Identities=21% Similarity=0.381 Sum_probs=23.2
Q ss_pred hcceecCceEEEEEEcCCCCeEEecCCC
Q 035470 34 EISVLCDAEVALIVFSTKGKLFEYSTDS 61 (62)
Q Consensus 34 ELs~Lc~~~v~~iv~~~~g~~~~~~s~~ 61 (62)
+|.-.+|++|++||.+..|..+-.++.+
T Consensus 135 ~l~~~~g~~v~VIItDt~gr~~R~G~t~ 162 (245)
T PRK13293 135 GLEELTGKKVGVIITDTNGRPFRKGQRG 162 (245)
T ss_pred HHHHHHCCCEEEEEEcCCCcccccCCcc
Confidence 4566789999999999999998877654
No 24
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=46.91 E-value=23 Score=20.24 Aligned_cols=26 Identities=12% Similarity=0.597 Sum_probs=19.5
Q ss_pred cceecCceE----EEEEEcCCCCeEEecCC
Q 035470 35 ISVLCDAEV----ALIVFSTKGKLFEYSTD 60 (62)
Q Consensus 35 Ls~Lc~~~v----~~iv~~~~g~~~~~~s~ 60 (62)
-+..||.++ .++.+..||+++-|+|+
T Consensus 5 ~CsFcG~~I~PGtG~m~Vr~Dg~v~~Fcss 34 (66)
T COG2075 5 VCSFCGKKIEPGTGIMYVRNDGKVLRFCSS 34 (66)
T ss_pred EecCcCCccCCCceEEEEecCCeEEEEech
Confidence 455677777 45666789999999986
No 25
>KOG0184 consensus 20S proteasome, regulatory subunit alpha type PSMA3/PRE10 [Posttranslational modification, protein turnover, chaperones]
Probab=44.86 E-value=14 Score=26.03 Aligned_cols=21 Identities=24% Similarity=0.485 Sum_probs=17.8
Q ss_pred ceecCceEEEEEEcCCCCeEE
Q 035470 36 SVLCDAEVALIVFSTKGKLFE 56 (62)
Q Consensus 36 s~Lc~~~v~~iv~~~~g~~~~ 56 (62)
|+=+|-|.+...|+|+|++|+
T Consensus 3 sIGtGyDls~s~fSpdGrvfQ 23 (254)
T KOG0184|consen 3 SIGTGYDLSASTFSPDGRVFQ 23 (254)
T ss_pred cccccccccceeeCCCCceeh
Confidence 445788999999999999986
No 26
>PRK09555 feoA ferrous iron transport protein A; Reviewed
Probab=42.31 E-value=53 Score=18.46 Aligned_cols=33 Identities=9% Similarity=0.156 Sum_probs=28.1
Q ss_pred chhhhhhhhcceecCceEEEEEEcCCCCeEEec
Q 035470 26 SGLLKKAHEISVLCDAEVALIVFSTKGKLFEYS 58 (62)
Q Consensus 26 ~GL~KKa~ELs~Lc~~~v~~iv~~~~g~~~~~~ 58 (62)
..+.++-.|+-++.|++|-++-..|-|.+..|.
T Consensus 20 ~~~~~rL~~mGl~pG~~V~v~~~aP~gdPi~i~ 52 (74)
T PRK09555 20 PAYRQKLLSLGMLPGSSFNVVRVAPLGDPIHIE 52 (74)
T ss_pred hHHHHHHHHcCCCCCCEEEEEEECCCCCCEEEE
Confidence 457889999999999999999999977766553
No 27
>PF14263 DUF4354: Domain of unknown function (DUF4354); PDB: 3NRF_B 3SB3_A.
Probab=38.82 E-value=17 Score=22.93 Aligned_cols=42 Identities=24% Similarity=0.324 Sum_probs=30.0
Q ss_pred eccccCcceehhhccchhhhhhhhcceecCceEEEEEEcCCCCeEEe
Q 035470 11 IENKINRQVTFSKRRSGLLKKAHEISVLCDAEVALIVFSTKGKLFEY 57 (62)
Q Consensus 11 I~~~~~R~~tf~KR~~GL~KKa~ELs~Lc~~~v~~iv~~~~g~~~~~ 57 (62)
+.++...+.||.=.-..+.++.-+|+.+ |+..|+|+|+-|..
T Consensus 41 v~~k~~ytktF~V~vaN~s~~~idLsk~-----Cf~a~~~~gk~f~l 82 (124)
T PF14263_consen 41 VGGKSFYTKTFDVTVANLSDKDIDLSKM-----CFKAYSPDGKEFKL 82 (124)
T ss_dssp ETTEEEEEEEEEEEEEE-SSS-EE-TT------EEEEEETTS-EEEE
T ss_pred ecCccceEEEEEEEEecCCCCccccccc-----hhhhccccCCEEEe
Confidence 4566777788888888888998888888 79999999987653
No 28
>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=38.25 E-value=17 Score=21.11 Aligned_cols=33 Identities=30% Similarity=0.537 Sum_probs=24.1
Q ss_pred hhhccchhhhh---------hhhcceecCceEEEEEEcCCCC
Q 035470 21 FSKRRSGLLKK---------AHEISVLCDAEVALIVFSTKGK 53 (62)
Q Consensus 21 f~KR~~GL~KK---------a~ELs~Lc~~~v~~iv~~~~g~ 53 (62)
|++-+++|..| +.|+.+-||.|.-++.+.|.|.
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 46666666554 5789999999999999888776
No 29
>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=38.21 E-value=22 Score=26.74 Aligned_cols=26 Identities=12% Similarity=0.469 Sum_probs=18.5
Q ss_pred cceecCceEE---------EEEEcCCCCeEEecCC
Q 035470 35 ISVLCDAEVA---------LIVFSTKGKLFEYSTD 60 (62)
Q Consensus 35 Ls~Lc~~~v~---------~iv~~~~g~~~~~~s~ 60 (62)
++-.|++.++ .....-+|+.|.|||+
T Consensus 382 ~c~vC~~p~~~~~~~~~~~~~~~ey~G~~y~FCS~ 416 (465)
T cd01057 382 LCNVCQVPCVFTEDLTAEAPRVLEYNGRKYHFCSE 416 (465)
T ss_pred CCCCCCCeeccccCcccccceEEEECCEEEEecCH
Confidence 6667777766 2233348999999997
No 30
>COG0139 HisI Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]
Probab=37.41 E-value=18 Score=22.56 Aligned_cols=25 Identities=28% Similarity=0.488 Sum_probs=20.0
Q ss_pred hhhhhhhcceecCceEEEEEEcCCC
Q 035470 28 LLKKAHEISVLCDAEVALIVFSTKG 52 (62)
Q Consensus 28 L~KKa~ELs~Lc~~~v~~iv~~~~g 52 (62)
=+.|..|+.+-||.|..++++.+.|
T Consensus 70 ~~q~v~~i~~DCD~Dall~~V~q~g 94 (111)
T COG0139 70 HTQKVVEIRLDCDGDALLLLVEQIG 94 (111)
T ss_pred ceEEEEEEEcCCCCCEEEEEEEeCC
Confidence 3445678999999999999888744
No 31
>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=36.99 E-value=41 Score=21.93 Aligned_cols=19 Identities=32% Similarity=0.677 Sum_probs=14.9
Q ss_pred eecCceEEEEEEcCCCCeE
Q 035470 37 VLCDAEVALIVFSTKGKLF 55 (62)
Q Consensus 37 ~Lc~~~v~~iv~~~~g~~~ 55 (62)
.-|+++|-+++|+++-+.|
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 4688899999999988755
No 32
>PHA02773 hypothetical protein; Provisional
Probab=36.39 E-value=90 Score=19.20 Aligned_cols=47 Identities=21% Similarity=0.471 Sum_probs=33.0
Q ss_pred cCcceehhhccchhhhhhhhccee-cCceEEEEEEcCCCCeEEecCCC
Q 035470 15 INRQVTFSKRRSGLLKKAHEISVL-CDAEVALIVFSTKGKLFEYSTDS 61 (62)
Q Consensus 15 ~~R~~tf~KR~~GL~KKa~ELs~L-c~~~v~~iv~~~~g~~~~~~s~~ 61 (62)
..-++...-..+-|+-.-.|++-. -+-|.|+.+|+..|.++.|-.++
T Consensus 15 ~e~qi~lr~kqkell~rffeiae~de~gdlciply~segdl~lfkkd~ 62 (112)
T PHA02773 15 EEKQIKLRPKQKELLIRFFEIAEKDEDGDLCIPLYDSEGDLFLFKKDA 62 (112)
T ss_pred hhhceeechhhHHHHHHHHHHheecCCCCEEEEeecCCCcEEEEeccc
Confidence 334445544455566666776644 58899999999999999987653
No 33
>PRK13294 F420-0--gamma-glutamyl ligase; Provisional
Probab=36.29 E-value=24 Score=26.34 Aligned_cols=28 Identities=18% Similarity=0.290 Sum_probs=23.5
Q ss_pred hcceecCceEEEEEEcCCCCeEEecCCC
Q 035470 34 EISVLCDAEVALIVFSTKGKLFEYSTDS 61 (62)
Q Consensus 34 ELs~Lc~~~v~~iv~~~~g~~~~~~s~~ 61 (62)
+|.-.+|++|+|||.+..|..+--++.+
T Consensus 135 ~l~~~~g~~v~vii~Dt~gr~~r~g~~~ 162 (448)
T PRK13294 135 GLRERLGVDVAVVVTDTMGRAWRNGQTD 162 (448)
T ss_pred HHHHHHCCCEEEEEecCCCCccccCccc
Confidence 4667799999999999999998777654
No 34
>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=36.07 E-value=12 Score=27.32 Aligned_cols=38 Identities=29% Similarity=0.359 Sum_probs=0.0
Q ss_pred cchhhhhhhhcceecCceEEE-EEEcCCCCeEEecCCCC
Q 035470 25 RSGLLKKAHEISVLCDAEVAL-IVFSTKGKLFEYSTDSW 62 (62)
Q Consensus 25 ~~GL~KKa~ELs~Lc~~~v~~-iv~~~~g~~~~~~s~~~ 62 (62)
..|++|=+.-..-+|++.-++ -+.+..|++.+|+||+.
T Consensus 53 qd~ilkym~~~m~~~n~~gfvy~~~~~~~k~~~~~s~sl 91 (354)
T PF04873_consen 53 QDGILKYMFPEMELCNAPGFVYTIISSSGKPVEGVSPSL 91 (354)
T ss_dssp ---------------------------------------
T ss_pred hhHHHHhhccccccccCceeeecCCCCCCCccCCcCCcc
Confidence 345565556678899999998 78889999999999973
No 35
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=35.43 E-value=29 Score=27.74 Aligned_cols=23 Identities=22% Similarity=0.368 Sum_probs=21.7
Q ss_pred ceecCceEEEEEEcCCCCeEEec
Q 035470 36 SVLCDAEVALIVFSTKGKLFEYS 58 (62)
Q Consensus 36 s~Lc~~~v~~iv~~~~g~~~~~~ 58 (62)
++|.|+-++|+.++++|.++++.
T Consensus 374 ~VLsgvtaGVi~~d~~g~i~t~N 396 (712)
T COG5000 374 AVLSGLTAGVIGFDNRGCITTVN 396 (712)
T ss_pred HHHhcCceeEEEEcCCCeeEeec
Confidence 69999999999999999999976
No 36
>PF12860 PAS_7: PAS fold
Probab=34.17 E-value=47 Score=18.84 Aligned_cols=19 Identities=21% Similarity=0.452 Sum_probs=15.4
Q ss_pred ceEEEEEEcCCCCeEEecC
Q 035470 41 AEVALIVFSTKGKLFEYST 59 (62)
Q Consensus 41 ~~v~~iv~~~~g~~~~~~s 59 (62)
...++++|+++|.+..|..
T Consensus 4 l~~Gv~v~D~~~rl~~~N~ 22 (115)
T PF12860_consen 4 LPQGVAVFDSDGRLVFWNQ 22 (115)
T ss_pred cCceEEEEcCCCeEEeEcH
Confidence 4568999999999988753
No 37
>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=33.87 E-value=47 Score=18.78 Aligned_cols=17 Identities=24% Similarity=0.227 Sum_probs=13.5
Q ss_pred EEEEEcCCCCeEEecCC
Q 035470 44 ALIVFSTKGKLFEYSTD 60 (62)
Q Consensus 44 ~~iv~~~~g~~~~~~s~ 60 (62)
.+.+++|+|..+.+.+|
T Consensus 112 ~~~~~DpdG~~ie~~~~ 128 (128)
T cd07242 112 ALFFEDPDGIRLELVAP 128 (128)
T ss_pred EEEEECCCCcEEEEEeC
Confidence 44566999999998876
No 38
>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=33.13 E-value=31 Score=23.68 Aligned_cols=41 Identities=20% Similarity=0.259 Sum_probs=28.8
Q ss_pred EeccccCcceehhhccchhhhhhhhcceecCceEEEEEEcCCCCe
Q 035470 10 RIENKINRQVTFSKRRSGLLKKAHEISVLCDAEVALIVFSTKGKL 54 (62)
Q Consensus 10 ~I~~~~~R~~tf~KR~~GL~KKa~ELs~Lc~~~v~~iv~~~~g~~ 54 (62)
.|+.--.|+..+.+...|- + +=.++-++|++++|++.+...
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 4555556776776666552 2 667899999999999875543
No 39
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=32.45 E-value=49 Score=20.25 Aligned_cols=20 Identities=20% Similarity=0.687 Sum_probs=14.2
Q ss_pred ceecCceEEEEEEcCCCCeEEecCCC
Q 035470 36 SVLCDAEVALIVFSTKGKLFEYSTDS 61 (62)
Q Consensus 36 s~Lc~~~v~~iv~~~~g~~~~~~s~~ 61 (62)
|.+||-+|. .|++|+|.+..
T Consensus 5 C~iCg~~I~------~gqlFTF~~kG 24 (101)
T PF09943_consen 5 CYICGKPIY------EGQLFTFTKKG 24 (101)
T ss_pred EEecCCeee------ecceEEEecCC
Confidence 456777765 68888887753
No 40
>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=32.33 E-value=4 Score=27.66 Aligned_cols=29 Identities=17% Similarity=0.357 Sum_probs=20.2
Q ss_pred hhcceecCceEEEEEEcCCCCeEEecCCC
Q 035470 33 HEISVLCDAEVALIVFSTKGKLFEYSTDS 61 (62)
Q Consensus 33 ~ELs~Lc~~~v~~iv~~~~g~~~~~~s~~ 61 (62)
.+|.-.+|.+|+++|.+++|..+..+++.
T Consensus 141 ~~l~~~~g~~v~ViI~Dt~gr~~r~G~~~ 169 (228)
T PF01996_consen 141 EELKERTGKDVGVIITDTNGRPWRLGQTG 169 (228)
T ss_dssp HHHHHHHS---EEEEEEEEEETTEECEEE
T ss_pred HHHHHHHCCceEEEEECCCCcEEecCCcc
Confidence 44667799999999999999887776543
No 41
>KOG0182 consensus 20S proteasome, regulatory subunit alpha type PSMA6/SCL1 [Posttranslational modification, protein turnover, chaperones]
Probab=31.86 E-value=45 Score=23.36 Aligned_cols=19 Identities=21% Similarity=0.562 Sum_probs=16.7
Q ss_pred ecCceEEEEEEcCCCCeEE
Q 035470 38 LCDAEVALIVFSTKGKLFE 56 (62)
Q Consensus 38 Lc~~~v~~iv~~~~g~~~~ 56 (62)
..|-|-.+.||+|.|++|+
T Consensus 6 ~agfDrhitIFspeGrLyQ 24 (246)
T KOG0182|consen 6 SAGFDRHITIFSPEGRLYQ 24 (246)
T ss_pred cCCccceEEEECCCceEEe
Confidence 4677889999999999996
No 42
>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=31.63 E-value=49 Score=18.61 Aligned_cols=30 Identities=17% Similarity=0.340 Sum_probs=19.2
Q ss_pred hhhhhhhcceec----CceEEEEEEcCCCCeEEe
Q 035470 28 LLKKAHEISVLC----DAEVALIVFSTKGKLFEY 57 (62)
Q Consensus 28 L~KKa~ELs~Lc----~~~v~~iv~~~~g~~~~~ 57 (62)
+++.|.+++... +..|+-++++++|++...
T Consensus 7 ~m~~a~~~a~~s~~~~~~~vgaviv~~~~~~i~~ 40 (102)
T PF00383_consen 7 FMRIAIELAKRSRPCGNFPVGAVIVDPDGKIIAT 40 (102)
T ss_dssp HHHHHHHHHHTHBTTTSSSEEEEEEETTTEEEEE
T ss_pred HHHHHHHHHHhccccCCCCEEEEEEeccCccEEE
Confidence 455665555444 778888888876665543
No 43
>KOG0641 consensus WD40 repeat protein [General function prediction only]
Probab=31.44 E-value=61 Score=23.33 Aligned_cols=33 Identities=30% Similarity=0.510 Sum_probs=24.9
Q ss_pred hhhhhh-cceecCceEE-EEEEcCCCCeEEecCCC
Q 035470 29 LKKAHE-ISVLCDAEVA-LIVFSTKGKLFEYSTDS 61 (62)
Q Consensus 29 ~KKa~E-Ls~Lc~~~v~-~iv~~~~g~~~~~~s~~ 61 (62)
-||-.| +.+|-|.++. .+-|+|.|.+|.-+|.|
T Consensus 19 ~k~~f~~i~~l~dsqairav~fhp~g~lyavgsns 53 (350)
T KOG0641|consen 19 EKKHFEAINILEDSQAIRAVAFHPAGGLYAVGSNS 53 (350)
T ss_pred cccceEEEEEecchhheeeEEecCCCceEEeccCC
Confidence 344444 6788888874 47889999999988865
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=30.55 E-value=70 Score=18.03 Aligned_cols=17 Identities=6% Similarity=0.245 Sum_probs=13.7
Q ss_pred EEEEEcCCCCeEEecCC
Q 035470 44 ALIVFSTKGKLFEYSTD 60 (62)
Q Consensus 44 ~~iv~~~~g~~~~~~s~ 60 (62)
.+.+.+|+|.+..++++
T Consensus 103 ~~~~~DPdGn~iei~~~ 119 (120)
T cd09011 103 VVRFYDPDKHIIEVGES 119 (120)
T ss_pred EEEEECCCCCEEEEecc
Confidence 45667999999998876
No 45
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=30.05 E-value=25 Score=26.39 Aligned_cols=46 Identities=20% Similarity=0.292 Sum_probs=37.2
Q ss_pred eEEeccccCcceehhhccchhhhhhhhcceecCceEEEEEEcCCCCeEEecC
Q 035470 8 LKRIENKINRQVTFSKRRSGLLKKAHEISVLCDAEVALIVFSTKGKLFEYST 59 (62)
Q Consensus 8 ik~I~~~~~R~~tf~KR~~GL~KKa~ELs~Lc~~~v~~iv~~~~g~~~~~~s 59 (62)
|+.+.|...-..+|.++..| |++.+|+.++-..+++...-+.+|..
T Consensus 18 i~~~~d~~~ps~~~~~~~~~------~~~~~~~g~~~~~~~~~~~~~~~~~~ 63 (412)
T COG5068 18 IQGDSDANIPSNTINRLSPG------ELSQQNDGKFDVMIFDSKHSVRVYSN 63 (412)
T ss_pred cccccccCCccccccccCcc------cchhhccCCcccccccccccccccCC
Confidence 77788888889999999999 99999999888777766555555543
No 46
>PF13082 DUF3931: Protein of unknown function (DUF3931)
Probab=29.58 E-value=29 Score=19.34 Aligned_cols=37 Identities=24% Similarity=0.341 Sum_probs=27.1
Q ss_pred cceeeEEeccccCcceehhhccchhhhhhhhcce--ecC
Q 035470 4 GRVQLKRIENKINRQVTFSKRRSGLLKKAHEISV--LCD 40 (62)
Q Consensus 4 ~ki~ik~I~~~~~R~~tf~KR~~GL~KKa~ELs~--Lc~ 40 (62)
+|-..--|.-+.+..-||+--+--.-.|.+|+|. |||
T Consensus 6 kkcnvisidgkkkksdtysypklvvenktyefssfvlcg 44 (66)
T PF13082_consen 6 KKCNVISIDGKKKKSDTYSYPKLVVENKTYEFSSFVLCG 44 (66)
T ss_pred ccccEEEeccccccCCcccCceEEEeCceEEEEEEEEEc
Confidence 4455556777777888888777777889999874 554
No 47
>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=28.00 E-value=82 Score=17.78 Aligned_cols=18 Identities=11% Similarity=0.386 Sum_probs=14.6
Q ss_pred EEEEEEcCCCCeEEecCC
Q 035470 43 VALIVFSTKGKLFEYSTD 60 (62)
Q Consensus 43 v~~iv~~~~g~~~~~~s~ 60 (62)
..+.+.+|+|....+.++
T Consensus 102 ~~~~~~DPdG~~ie~~~~ 119 (120)
T cd08350 102 REFALVDPDGNLLRFGQP 119 (120)
T ss_pred eEEEEECCCCCEEEeecC
Confidence 356788999999998875
No 48
>PF01849 NAC: NAC domain; InterPro: IPR002715 Nascent polypeptide-associated complex (NAC) is among the first ribosome-associated entities to bind the nascent polypeptide after peptide bond formation. The nascent polypeptide-associated complex (NAC) of yeast functions in the targeting process of ribosomes to the ER membrane []. NAC may prevent binding of ribosome nascent chains (RNCs) without a signal sequence to yeast membranes.; PDB: 3MCE_D 3MCB_A 3LKX_B 1TR8_B.
Probab=26.67 E-value=37 Score=18.06 Aligned_cols=18 Identities=11% Similarity=0.348 Sum_probs=12.5
Q ss_pred EEEEcCCCCeEEecCCCC
Q 035470 45 LIVFSTKGKLFEYSTDSW 62 (62)
Q Consensus 45 ~iv~~~~g~~~~~~s~~~ 62 (62)
+.++.++|..+.|..|.|
T Consensus 22 V~i~~~dg~~~~~~~P~V 39 (58)
T PF01849_consen 22 VTIRKDDGTVFVFNNPEV 39 (58)
T ss_dssp EEEEETTTEEEEEESEEE
T ss_pred EEEEECCceEEEEcCCeE
Confidence 445556788888887754
No 49
>KOG0278 consensus Serine/threonine kinase receptor-associated protein [Lipid transport and metabolism]
Probab=26.60 E-value=77 Score=23.04 Aligned_cols=19 Identities=26% Similarity=0.564 Sum_probs=15.1
Q ss_pred EEEEEEcCCCCeEEecCCC
Q 035470 43 VALIVFSTKGKLFEYSTDS 61 (62)
Q Consensus 43 v~~iv~~~~g~~~~~~s~~ 61 (62)
|.-+.|+|+|.+|.-+|.|
T Consensus 270 VhcVrFSPdGE~yAsGSED 288 (334)
T KOG0278|consen 270 VHCVRFSPDGELYASGSED 288 (334)
T ss_pred eEEEEECCCCceeeccCCC
Confidence 3457889999999988864
No 50
>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=26.43 E-value=76 Score=18.77 Aligned_cols=36 Identities=8% Similarity=0.151 Sum_probs=26.9
Q ss_pred cchhhhhhhhcceecCceEEEEE-EcCCCCeEEecCC
Q 035470 25 RSGLLKKAHEISVLCDAEVALIV-FSTKGKLFEYSTD 60 (62)
Q Consensus 25 ~~GL~KKa~ELs~Lc~~~v~~iv-~~~~g~~~~~~s~ 60 (62)
-..|..|..|++-+-.-...-+= .++.|.+.+++|+
T Consensus 22 ~e~L~~~v~~~c~~~~~q~ft~kw~DEEGDp~tiSS~ 58 (83)
T cd06404 22 LEELCNEVRDMCRFHNDQPFTLKWIDEEGDPCTISSQ 58 (83)
T ss_pred HHHHHHHHHHHhCCCCCCcEEEEEECCCCCceeecCH
Confidence 36788999999888665444443 4889999999885
No 51
>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=26.41 E-value=89 Score=18.88 Aligned_cols=28 Identities=14% Similarity=0.315 Sum_probs=18.1
Q ss_pred hhhhhcceec------CceEEEEEEcCCCCeEEe
Q 035470 30 KKAHEISVLC------DAEVALIVFSTKGKLFEY 57 (62)
Q Consensus 30 KKa~ELs~Lc------~~~v~~iv~~~~g~~~~~ 57 (62)
+.|.|++-.+ +..|.-++++++|++..-
T Consensus 2 ~~al~~A~~~~~~~~~~~pvGaviv~~~g~iv~~ 35 (115)
T cd01284 2 RRALELAEKGRGLTSPNPPVGCVIVDDDGEIVGE 35 (115)
T ss_pred HHHHHHHHhcccccCCCCCEEEEEEeCCCeEEEE
Confidence 4455555544 667877777777887654
No 52
>KOG0712 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=25.76 E-value=1.1e+02 Score=22.28 Aligned_cols=40 Identities=30% Similarity=0.505 Sum_probs=31.9
Q ss_pred ceehhhccchhhhhhhhcc---eecCceEEEEEEcCCCCeEEecCC
Q 035470 18 QVTFSKRRSGLLKKAHEIS---VLCDAEVALIVFSTKGKLFEYSTD 60 (62)
Q Consensus 18 ~~tf~KR~~GL~KKa~ELs---~Lc~~~v~~iv~~~~g~~~~~~s~ 60 (62)
...|.+|..+|+.+. .++ -||+-...+- ..+|......++
T Consensus 244 h~~F~Rrg~dL~~~~-~i~l~eal~G~~~~~~--~ldGr~l~~~~~ 286 (337)
T KOG0712|consen 244 HPGFDRRGSDLYRKL-TISLVEALCGFQRVWE--TLDGRLLKLSSK 286 (337)
T ss_pred cccceecccccceee-ecchhhccccceEEEE--ccCCceEEEecC
Confidence 789999999999888 888 7888666655 777877776665
No 53
>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=25.69 E-value=32 Score=18.11 Aligned_cols=22 Identities=27% Similarity=0.650 Sum_probs=17.0
Q ss_pred hhhhhhhcceecCceEEEEEEc
Q 035470 28 LLKKAHEISVLCDAEVALIVFS 49 (62)
Q Consensus 28 L~KKa~ELs~Lc~~~v~~iv~~ 49 (62)
|.+.+..-+=||+++..+.+|.
T Consensus 2 L~~Rs~~kCELC~a~~~L~vy~ 23 (47)
T smart00782 2 LLARCESKCELCGSDSPLVVYA 23 (47)
T ss_pred hhHHcCCcccCcCCCCCceEEe
Confidence 4556667788999999888883
No 54
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, 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.
Probab=25.05 E-value=86 Score=18.58 Aligned_cols=36 Identities=14% Similarity=0.182 Sum_probs=28.7
Q ss_pred cchhhhhhhhcceecCceEEEEEEcCCCCeEEecCC
Q 035470 25 RSGLLKKAHEISVLCDAEVALIVFSTKGKLFEYSTD 60 (62)
Q Consensus 25 ~~GL~KKa~ELs~Lc~~~v~~iv~~~~g~~~~~~s~ 60 (62)
..+|..|..+|--|....+++--++++|...+-+|.
T Consensus 22 ~~~L~~kl~~Lf~lp~~~~~vtYiDeD~D~ITlssd 57 (82)
T cd06397 22 WEALASKLENLYNLPEIKVGVTYIDNDNDEITLSSN 57 (82)
T ss_pred HHHHHHHHHHHhCCChhHeEEEEEcCCCCEEEecch
Confidence 358889999988888766777777889888887764
No 55
>PF09695 YtfJ_HI0045: Bacterial protein of unknown function (YtfJ_HI0045); InterPro: IPR006513 These are sequences from gammaproteobacteria that are related to the Escherichia coli protein, YtfJ.
Probab=24.98 E-value=75 Score=20.94 Aligned_cols=36 Identities=25% Similarity=0.406 Sum_probs=26.6
Q ss_pred eehhhccchhhhhhhhcceecCceEEEEEEcCCCCeEEe
Q 035470 19 VTFSKRRSGLLKKAHEISVLCDAEVALIVFSTKGKLFEY 57 (62)
Q Consensus 19 ~tf~KR~~GL~KKa~ELs~Lc~~~v~~iv~~~~g~~~~~ 57 (62)
++|--=.+|..++|+.|.- -.-++||.+.+|++..+
T Consensus 105 s~~vlD~~G~~~~aW~L~~---~~SaiiVlDK~G~V~F~ 140 (160)
T PF09695_consen 105 SQFVLDSNGVVRKAWQLQE---ESSAIIVLDKQGKVQFV 140 (160)
T ss_pred cEEEEcCCCceeccccCCC---CCceEEEEcCCccEEEE
Confidence 3455556899999999973 34467888999988655
No 56
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=24.42 E-value=1.5e+02 Score=18.28 Aligned_cols=55 Identities=25% Similarity=0.369 Sum_probs=29.9
Q ss_pred CCccceeeEEeccccCcceehhhccchhhhhhhhcceecCce----EEEEEEcCCCCeEEec
Q 035470 1 MGRGRVQLKRIENKINRQVTFSKRRSGLLKKAHEISVLCDAE----VALIVFSTKGKLFEYS 58 (62)
Q Consensus 1 mgR~ki~ik~I~~~~~R~~tf~KR~~GL~KKa~ELs~Lc~~~----v~~iv~~~~g~~~~~~ 58 (62)
|||++.+.+.|... |+..+.|+-.. ..=-+|.++.|-++ ++.++.+..|.-|.+-
T Consensus 1 MG~rr~krr~~ik~--~~~~L~k~FtC-p~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~e 59 (104)
T COG4888 1 MGRRRRKRRKIIKR--RPQVLPKTFTC-PRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECE 59 (104)
T ss_pred CCcccccccccCcc--cCccCCceEec-CccCCeeeeEEEEEecCceeEEEcccCcceEEEe
Confidence 89999887776432 22223333222 22234555555443 4666667777777654
No 57
>cd07264 Glo_EDI_BRP_like_15 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=24.31 E-value=98 Score=17.19 Aligned_cols=16 Identities=25% Similarity=0.247 Sum_probs=12.7
Q ss_pred EEEEcCCCCeEEecCC
Q 035470 45 LIVFSTKGKLFEYSTD 60 (62)
Q Consensus 45 ~iv~~~~g~~~~~~s~ 60 (62)
..+.+|+|..+.+.+|
T Consensus 110 ~~~~DPdG~~~~~~~~ 125 (125)
T cd07264 110 AYVRDINGFLIELCSP 125 (125)
T ss_pred EEEECCCCCEEEEecC
Confidence 3667999999888775
No 58
>COG1918 FeoA Fe2+ transport system protein A [Inorganic ion transport and metabolism]
Probab=23.98 E-value=1.5e+02 Score=16.84 Aligned_cols=31 Identities=13% Similarity=0.266 Sum_probs=26.9
Q ss_pred chhhhhhhhcceecCceEEEEEEcCCCCeEE
Q 035470 26 SGLLKKAHEISVLCDAEVALIVFSTKGKLFE 56 (62)
Q Consensus 26 ~GL~KKa~ELs~Lc~~~v~~iv~~~~g~~~~ 56 (62)
+++.+|-.|+-+.-|+++.++--.|-|.+..
T Consensus 21 ~~~~~RL~~mG~~~G~~i~vi~~aplgdPi~ 51 (75)
T COG1918 21 NGLRRRLLSMGIVPGASITVVRKAPLGDPIL 51 (75)
T ss_pred HHHHHHHHHcCCCCCCEEEEEEecCCCCCEE
Confidence 4899999999999999999999988875543
No 59
>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=23.28 E-value=64 Score=22.43 Aligned_cols=25 Identities=12% Similarity=0.360 Sum_probs=20.0
Q ss_pred ceecCceEEEEEEcC--CCCeEEecCC
Q 035470 36 SVLCDAEVALIVFST--KGKLFEYSTD 60 (62)
Q Consensus 36 s~Lc~~~v~~iv~~~--~g~~~~~~s~ 60 (62)
+++-|.+++++.|++ +||.|+...+
T Consensus 68 ~~~~G~n~~i~ayG~tgSGKT~Tm~G~ 94 (341)
T cd01372 68 GLFEGYNATVLAYGQTGSGKTYTMGTA 94 (341)
T ss_pred HHhCCCccceeeecCCCCCCcEEecCC
Confidence 457899999999975 6799987543
No 60
>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=23.06 E-value=73 Score=20.22 Aligned_cols=21 Identities=19% Similarity=0.420 Sum_probs=16.5
Q ss_pred eecCceEEEEEEcCC--CCeEEe
Q 035470 37 VLCDAEVALIVFSTK--GKLFEY 57 (62)
Q Consensus 37 ~Lc~~~v~~iv~~~~--g~~~~~ 57 (62)
++.|-+.+++.|+++ ||.|+-
T Consensus 19 ~~~G~n~~i~~yG~tGsGKT~Tm 41 (186)
T cd01363 19 ALDGYNVCIFAYGQTGSGKTYTM 41 (186)
T ss_pred HhCCcceeEEEECCCCCcceEec
Confidence 457899999999865 787764
No 61
>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=22.76 E-value=1.2e+02 Score=17.16 Aligned_cols=17 Identities=12% Similarity=0.315 Sum_probs=13.5
Q ss_pred EEEEEEcCCCCeEEecC
Q 035470 43 VALIVFSTKGKLFEYST 59 (62)
Q Consensus 43 v~~iv~~~~g~~~~~~s 59 (62)
..+.+.+|+|++..+++
T Consensus 97 r~f~~~DPdGn~~~~~~ 113 (113)
T cd08356 97 REFFLHDPSGVLWHIGQ 113 (113)
T ss_pred EEEEEECCCccEEEeeC
Confidence 56778899999988763
No 62
>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=22.73 E-value=1.5e+02 Score=16.25 Aligned_cols=19 Identities=16% Similarity=-0.090 Sum_probs=14.6
Q ss_pred eEEEEEEcCCCCeEEecCC
Q 035470 42 EVALIVFSTKGKLFEYSTD 60 (62)
Q Consensus 42 ~v~~iv~~~~g~~~~~~s~ 60 (62)
...+.+.+|+|..+.+++.
T Consensus 104 ~~~~~~~DP~G~~~~l~~~ 122 (122)
T cd07246 104 DRYGGVRDPFGHRWWIATH 122 (122)
T ss_pred ceEEEEECCCCCEEEEecC
Confidence 3466788999999988763
No 63
>cd07244 FosA FosA, a Fosfomycin resistance protein, catalyzes the addition of glutathione to the antibiotic fosfomycin, making it inactive. This subfamily family contains FosA, a fosfomycin resistant protein. Fosfomycin inhibits the enzyme UDP-N-acetylglucosamine-3-enolpyruvyltransferase (MurA), which catalyzes the first committed step in bacterial cell wall biosynthesis. FosA, catalyzes the addition of glutathione to the antibiotic fosfomycin, (1R,2S)-epoxypropylphosphonic acid, making it inactive. FosA is a Mn(II) dependent enzyme. It is evolutionarily related to glyoxalase I and type I extradiol dioxygenases.
Probab=22.60 E-value=1.1e+02 Score=17.37 Aligned_cols=18 Identities=17% Similarity=0.342 Sum_probs=14.4
Q ss_pred EEEEEcCCCCeEEecCCC
Q 035470 44 ALIVFSTKGKLFEYSTDS 61 (62)
Q Consensus 44 ~~iv~~~~g~~~~~~s~~ 61 (62)
.+.+.+|+|..+.+.+.+
T Consensus 94 ~~~f~DPdG~~ie~~~~~ 111 (121)
T cd07244 94 SFYFLDPDGHKLELHVGS 111 (121)
T ss_pred EEEEECCCCCEEEEEeCC
Confidence 566779999999988764
No 64
>PF13186 SPASM: Iron-sulfur cluster-binding domain
Probab=22.30 E-value=81 Score=15.77 Aligned_cols=19 Identities=16% Similarity=0.440 Sum_probs=11.8
Q ss_pred cCceEEEEEEcCCCCeEEe
Q 035470 39 CDAEVALIVFSTKGKLFEY 57 (62)
Q Consensus 39 c~~~v~~iv~~~~g~~~~~ 57 (62)
|++---.+.++++|.+|--
T Consensus 1 C~~~~~~~~I~~dG~v~pC 19 (64)
T PF13186_consen 1 CGAGWNSLYIDPDGDVYPC 19 (64)
T ss_pred CCCcCeEEEEeeCccEEeC
Confidence 3444445666788888764
No 65
>PF09729 Gti1_Pac2: Gti1/Pac2 family; InterPro: IPR018608 In Schizosaccharomyces pombe (Fission yeast) the gti1 protein promotes the onset of gluconate uptake upon glucose starvation []. In S. pombe the Pac2 protein controls the onset of sexual development, by inhibiting the expression of ste11, in a pathway that is independent of the cAMP cascade [].
Probab=22.23 E-value=53 Score=21.68 Aligned_cols=30 Identities=23% Similarity=0.420 Sum_probs=24.7
Q ss_pred ehhhccchhhhhhhhcceecCceEEEEEEc
Q 035470 20 TFSKRRSGLLKKAHEISVLCDAEVALIVFS 49 (62)
Q Consensus 20 tf~KR~~GL~KKa~ELs~Lc~~~v~~iv~~ 49 (62)
.+.-+..||.||...+.+-.+....||-|-
T Consensus 137 ~~~~K~~GLiKKT~Si~~~~~~~~HLISYY 166 (168)
T PF09729_consen 137 SYPFKPDGLIKKTISITTKQGQKLHLISYY 166 (168)
T ss_pred CCccCCCCeeEEEEEEEecCCCeEEEEEEe
Confidence 466778999999999988878888888773
No 66
>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=22.21 E-value=79 Score=22.28 Aligned_cols=22 Identities=18% Similarity=0.377 Sum_probs=18.1
Q ss_pred ceecCceEEEEEEcC--CCCeEEe
Q 035470 36 SVLCDAEVALIVFST--KGKLFEY 57 (62)
Q Consensus 36 s~Lc~~~v~~iv~~~--~g~~~~~ 57 (62)
+++-|.+++++.|++ +||.|+-
T Consensus 83 ~~l~G~n~~i~ayGqtGSGKT~Tm 106 (356)
T cd01365 83 HAFEGYNVCLFAYGQTGSGKSYTM 106 (356)
T ss_pred HHhCCCceEEEEecCCCCCCeEEe
Confidence 468899999999975 6788874
No 67
>PRK09732 hypothetical protein; Provisional
Probab=22.18 E-value=1.1e+02 Score=19.17 Aligned_cols=28 Identities=21% Similarity=0.229 Sum_probs=20.6
Q ss_pred hhhhcceecCceEEEEEEcCCCCeEEec
Q 035470 31 KAHEISVLCDAEVALIVFSTKGKLFEYS 58 (62)
Q Consensus 31 Ka~ELs~Lc~~~v~~iv~~~~g~~~~~~ 58 (62)
.|.+-+.-=+..+++.|.++.|.+..|-
T Consensus 18 aA~~~A~~~g~~v~iaVvD~~G~l~a~~ 45 (134)
T PRK09732 18 AGQEEAQKNNWSVSIAVADDGGHLLALS 45 (134)
T ss_pred HHHHHHHHhCCCEEEEEEcCCCCEEEEE
Confidence 3344444447889999999999998774
No 68
>PF14009 DUF4228: Domain of unknown function (DUF4228)
Probab=21.92 E-value=1.1e+02 Score=18.46 Aligned_cols=22 Identities=18% Similarity=0.329 Sum_probs=15.7
Q ss_pred cCceEEEEEEcCCCCeEEecCC
Q 035470 39 CDAEVALIVFSTKGKLFEYSTD 60 (62)
Q Consensus 39 c~~~v~~iv~~~~g~~~~~~s~ 60 (62)
++...++-|..++|++..|..|
T Consensus 12 ~~~~~~vkvv~~~G~v~~~~~p 33 (181)
T PF14009_consen 12 SSSAATVKVVHPDGKVEEFKRP 33 (181)
T ss_pred cCCCceEEEEcCCCcEEEeCCC
Confidence 3445566666689999999765
No 69
>PF08796 DUF1797: Protein of unknown function (DUF1797); InterPro: IPR014904 The function of this protein is unknown. It forms a central anti-parallel beta sheet with flanking alpha helical regions. ; PDB: 2FFG_B.
Probab=21.32 E-value=1.4e+02 Score=16.96 Aligned_cols=18 Identities=22% Similarity=0.421 Sum_probs=14.1
Q ss_pred cCceEEEEEEcCCCCeEE
Q 035470 39 CDAEVALIVFSTKGKLFE 56 (62)
Q Consensus 39 c~~~v~~iv~~~~g~~~~ 56 (62)
-|+++|.|.|++....|+
T Consensus 24 ~G~~~c~V~y~~~t~~F~ 41 (67)
T PF08796_consen 24 EGVEVCTVTYDQETETFE 41 (67)
T ss_dssp TTEEEEEEEEETTTTEEE
T ss_pred CCEEEEEEEEECCCCeEE
Confidence 588999999987666654
No 70
>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=21.07 E-value=43 Score=20.64 Aligned_cols=24 Identities=29% Similarity=0.670 Sum_probs=17.9
Q ss_pred ceeeEEe-ccccCcceehhhccchh
Q 035470 5 RVQLKRI-ENKINRQVTFSKRRSGL 28 (62)
Q Consensus 5 ki~ik~I-~~~~~R~~tf~KR~~GL 28 (62)
+++++-+ +|.++-.+.|.||-.|+
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 4666665 67788899999999996
No 71
>PHA02757 hypothetical protein; Provisional
Probab=20.95 E-value=1.3e+02 Score=17.30 Aligned_cols=18 Identities=22% Similarity=0.434 Sum_probs=14.7
Q ss_pred eEEEEEEcCC-CCeEEecC
Q 035470 42 EVALIVFSTK-GKLFEYST 59 (62)
Q Consensus 42 ~v~~iv~~~~-g~~~~~~s 59 (62)
++|+|=.+|+ |.+++|+-
T Consensus 46 K~CiiE~de~sGml~s~C~ 64 (75)
T PHA02757 46 KACIIEIDEDSGMLFSQCD 64 (75)
T ss_pred ceEEEEEcCCCCcEEEecC
Confidence 5788888875 99999875
No 72
>cd03750 proteasome_alpha_type_2 proteasome_alpha_type_2. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=20.74 E-value=26 Score=23.06 Aligned_cols=13 Identities=46% Similarity=0.756 Sum_probs=10.0
Q ss_pred EEEEEcCCCCeEE
Q 035470 44 ALIVFSTKGKLFE 56 (62)
Q Consensus 44 ~~iv~~~~g~~~~ 56 (62)
.+-+|+|+|++|+
T Consensus 4 ~~t~fsp~Grl~Q 16 (227)
T cd03750 4 SLTTFSPSGKLVQ 16 (227)
T ss_pred CCceECCCCeEhH
Confidence 3567999999874
No 73
>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]
Probab=20.26 E-value=45 Score=22.73 Aligned_cols=25 Identities=32% Similarity=0.353 Sum_probs=18.4
Q ss_pred eehhhccchhhhhh--hhcceecCceE
Q 035470 19 VTFSKRRSGLLKKA--HEISVLCDAEV 43 (62)
Q Consensus 19 ~tf~KR~~GL~KKa--~ELs~Lc~~~v 43 (62)
++=.+=-+||++|| .|+.-.+|++-
T Consensus 133 vce~RDpKGLYkKAr~GeI~~fTGid~ 159 (197)
T COG0529 133 VCERRDPKGLYKKARAGEIKNFTGIDS 159 (197)
T ss_pred HHHhcCchHHHHHHHcCCCCCCcCCCC
Confidence 33344568999998 67888888774
No 74
>PF03989 DNA_gyraseA_C: DNA gyrase C-terminal domain, beta-propeller; InterPro: IPR006691 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils []. This entry represents the beta-pinwheel repeat found at the C-terminal end of subunit A of topoisomerase IV (ParC) and subunit A of DNA gyrase (GyrA). DNA gyrase is the topoisomerase II found primarily in bacteria and archaea that consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. This is distinct from the topoisomerase II found in most eukaryotes, which consists of a single polypeptide, with the N- and C-terminal regions corresponding to gyrB and gyrA, respectively, and which is not represented in this entry. The ability of DNA gyrase to introduce negative supercoils into DNA is mediated in part by the C-terminal domain of subunit A, which forms a beta-pinwheel fold that is similar to a beta-propeller but with a different blade topology, and which forms a superhelical spiral domain [, ]. This beta-pinwheel is capable of bending DNA by over 180 degrees over a 40 bp region, possibly by wrapping the DNA around the GyrA C-terminal beta-pinwheel domain. In topoisomerase IV, although the C-terminal domain forms a similar superhelical spiral to that of DNA gyrase A, it assembles as a broken form of a beta-pinwheel as distinct from that of gyrA, due to the absence of a DNA gyrase-specific GyrA box motif []. This difference may account for parC being less efficient than gyrA in mediating DNA-bending, leading to their divergence in terms of activity, where topoisomerase IV acts to relax positive supercoils, and DNA gyrase acts to introduce negative supercoils []. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome; PDB: 3L6V_A 3UC1_A 1ZI0_B 1SUU_A 1ZVU_A 1ZVT_B 3NO0_B.
Probab=20.00 E-value=86 Score=15.35 Aligned_cols=16 Identities=6% Similarity=0.304 Sum_probs=11.7
Q ss_pred EEEEcCCCCeEEecCC
Q 035470 45 LIVFSTKGKLFEYSTD 60 (62)
Q Consensus 45 ~iv~~~~g~~~~~~s~ 60 (62)
+++++.+|..+.+...
T Consensus 3 il~~T~~G~~~r~~~~ 18 (48)
T PF03989_consen 3 ILLITSNGYVKRIPLS 18 (48)
T ss_dssp EEEEETTSEEEEEEGG
T ss_pred EEEEeCCCeEEEeeec
Confidence 5677888888877643
Done!