Query 040972
Match_columns 87
No_of_seqs 122 out of 1065
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 02:34:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040972.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040972hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00265 MADS_MEF2_like MEF2 (m 100.0 7E-35 1.5E-39 178.7 4.3 77 2-78 1-77 (77)
2 KOG0014 MADS box transcription 100.0 1.5E-34 3.3E-39 199.1 4.8 85 1-85 1-87 (195)
3 cd00266 MADS_SRF_like SRF-like 100.0 3E-32 6.4E-37 169.0 5.2 81 2-82 1-82 (83)
4 smart00432 MADS MADS domain. 100.0 3.2E-30 6.9E-35 151.2 4.5 59 2-60 1-59 (59)
5 cd00120 MADS MADS: MCM1, Agamo 100.0 1.6E-29 3.6E-34 148.2 3.4 59 2-60 1-59 (59)
6 PF00319 SRF-TF: SRF-type tran 99.9 1E-27 2.2E-32 137.0 0.8 51 9-59 1-51 (51)
7 KOG0015 Regulator of arginine 99.8 1E-21 2.2E-26 145.0 2.5 65 2-66 63-127 (338)
8 COG5068 ARG80 Regulator of arg 99.6 1.7E-15 3.6E-20 115.6 3.0 68 1-68 81-148 (412)
9 PF10491 Nrf1_DNA-bind: NLS-bi 76.7 3.7 8E-05 29.6 3.4 48 26-73 35-89 (214)
10 PF09151 DUF1936: Domain of un 73.2 4.4 9.5E-05 20.9 2.2 24 34-57 2-25 (36)
11 PF10584 Proteasome_A_N: Prote 61.4 1.2 2.7E-05 21.2 -1.2 13 44-56 4-16 (23)
12 KOG4637 Adaptor for phosphoino 55.6 8.3 0.00018 30.4 1.8 47 33-79 367-418 (464)
13 PF09941 DUF2173: Uncharacteri 52.7 27 0.00059 22.6 3.6 37 32-69 3-42 (108)
14 TIGR01916 F420_cofE F420-0:gam 50.1 15 0.00031 27.0 2.3 27 33-59 133-159 (243)
15 COG4888 Uncharacterized Zn rib 47.6 11 0.00024 24.3 1.1 68 1-71 1-79 (104)
16 PF14263 DUF4354: Domain of un 46.2 7.4 0.00016 25.8 0.2 42 11-57 41-82 (124)
17 PRK14891 50S ribosomal protein 44.8 24 0.00053 23.6 2.5 46 34-80 5-54 (131)
18 PRK13293 F420-0--gamma-glutamy 43.4 22 0.00048 26.1 2.4 27 33-59 134-160 (245)
19 PF11232 Med25: Mediator compl 41.5 37 0.0008 23.3 3.1 23 37-59 109-132 (152)
20 COG2075 RPL24A Ribosomal prote 41.1 49 0.0011 19.7 3.2 44 35-79 5-52 (66)
21 COG5000 NtrY Signal transducti 40.7 30 0.00065 29.0 2.9 23 36-58 374-396 (712)
22 PF14009 DUF4228: Domain of un 38.1 49 0.0011 21.5 3.3 34 39-72 12-46 (181)
23 cd06397 PB1_UP1 Uncharacterize 36.0 1.1E+02 0.0023 19.0 4.2 56 15-70 10-68 (82)
24 COG0139 HisI Phosphoribosyl-AM 35.6 11 0.00023 24.7 -0.3 27 27-53 69-95 (111)
25 PRK09555 feoA ferrous iron tra 34.3 59 0.0013 19.2 2.8 32 26-57 20-51 (74)
26 PF01246 Ribosomal_L24e: Ribos 33.4 60 0.0013 19.4 2.8 33 34-66 4-40 (71)
27 PF04945 YHS: YHS domain; Int 31.4 66 0.0014 17.0 2.5 26 39-64 6-34 (47)
28 cd01365 KISc_KIF1A_KIF1B Kines 31.3 46 0.001 25.0 2.5 24 36-59 83-109 (356)
29 PF13540 RCC1_2: Regulator of 30.7 38 0.00083 16.3 1.4 22 37-59 4-25 (30)
30 PRK09822 lipopolysaccharide co 30.2 30 0.00066 25.7 1.3 41 18-59 117-160 (269)
31 COG4917 EutP Ethanolamine util 29.6 42 0.0009 22.9 1.8 24 34-57 58-81 (148)
32 cd00472 Ribosomal_L24e_L24 Rib 29.4 53 0.0012 18.6 2.0 33 34-66 4-40 (54)
33 PF00383 dCMP_cyt_deam_1: Cyti 29.4 83 0.0018 18.7 3.0 28 27-54 6-37 (102)
34 PF01996 F420_ligase: F420-0:G 29.0 15 0.00033 26.3 -0.5 27 33-59 141-167 (228)
35 KOG0183 20S proteasome, regula 28.9 39 0.00084 24.8 1.6 19 41-59 4-24 (249)
36 COG4831 Roadblock/LC7 domain [ 28.8 81 0.0018 20.3 2.9 29 30-59 3-31 (109)
37 COG3411 Ferredoxin [Energy pro 27.9 98 0.0021 18.3 3.0 28 44-71 18-46 (64)
38 smart00252 SH2 Src homology 2 27.6 1E+02 0.0022 17.6 3.1 42 33-74 37-83 (84)
39 PRK13294 F420-0--gamma-glutamy 26.9 52 0.0011 26.0 2.2 27 33-59 134-160 (448)
40 PRK00807 50S ribosomal protein 26.4 1.1E+02 0.0023 17.0 2.9 44 34-78 2-49 (52)
41 PF01502 PRA-CH: Phosphoribosy 26.2 16 0.00034 22.2 -0.7 25 29-53 39-63 (75)
42 KOG2292 Oligosaccharyltransfer 26.2 75 0.0016 26.6 3.0 32 29-63 584-615 (751)
43 cd00106 KISc Kinesin motor dom 26.0 63 0.0014 23.6 2.4 24 36-59 73-99 (328)
44 smart00782 PhnA_Zn_Ribbon PhnA 25.5 34 0.00074 18.8 0.7 22 28-49 2-23 (47)
45 cd01284 Riboflavin_deaminase-r 25.3 1E+02 0.0022 19.7 3.0 28 29-56 1-34 (115)
46 cd03063 TRX_Fd_FDH_beta TRX-li 24.6 1.6E+02 0.0034 18.2 3.7 36 38-73 44-81 (92)
47 cd01668 TGS_RelA_SpoT TGS_RelA 24.4 1.2E+02 0.0026 15.9 2.9 24 46-69 2-26 (60)
48 PF02092 tRNA_synt_2f: Glycyl- 24.3 17 0.00038 29.5 -0.9 66 19-87 211-281 (548)
49 PF10662 PduV-EutP: Ethanolami 24.1 68 0.0015 21.5 2.1 24 35-58 58-81 (143)
50 PF06020 Roughex: Drosophila r 24.0 36 0.00078 26.0 0.7 16 36-51 183-198 (334)
51 cd01371 KISc_KIF3 Kinesin moto 23.2 83 0.0018 23.4 2.6 24 36-59 76-102 (333)
52 PF13252 DUF4043: Protein of u 23.1 33 0.00072 26.2 0.4 29 31-59 270-300 (341)
53 TIGR03726 strep_RK_lipo putati 23.0 31 0.00066 17.9 0.2 16 29-44 3-18 (34)
54 COG5068 ARG80 Regulator of arg 23.0 49 0.0011 26.2 1.4 46 8-59 18-63 (412)
55 PF02824 TGS: TGS domain; Int 22.9 1.5E+02 0.0033 16.4 3.1 24 45-68 1-25 (60)
56 PF15119 APOC4: Apolipoprotein 22.7 43 0.00094 21.2 0.8 19 22-40 76-96 (99)
57 cd01368 KISc_KIF23_like Kinesi 22.5 80 0.0017 23.7 2.4 25 36-60 83-110 (345)
58 PF08796 DUF1797: Protein of u 22.4 89 0.0019 18.5 2.1 18 39-56 24-41 (67)
59 cd02980 TRX_Fd_family Thioredo 22.4 1.2E+02 0.0027 16.9 2.7 29 39-68 47-76 (77)
60 PF06574 FAD_syn: FAD syntheta 22.3 97 0.0021 20.7 2.6 26 26-51 22-47 (157)
61 PF03927 NapD: NapD protein; 22.1 1E+02 0.0023 18.3 2.4 37 32-70 21-58 (79)
62 cd01376 KISc_KID_like Kinesin 21.8 93 0.002 22.9 2.6 21 36-56 75-97 (319)
63 smart00129 KISc Kinesin motor, 21.7 85 0.0019 23.1 2.4 23 37-59 75-100 (335)
64 COG1918 FeoA Fe2+ transport sy 21.6 1.3E+02 0.0028 18.0 2.7 31 26-56 21-51 (75)
65 COG1438 ArgR Arginine represso 21.5 53 0.0011 22.4 1.1 18 33-50 118-135 (150)
66 PF07676 PD40: WD40-like Beta 21.5 59 0.0013 16.0 1.1 18 42-59 10-27 (39)
67 PF00360 PHY: Phytochrome regi 21.3 85 0.0018 21.5 2.2 38 26-65 20-58 (182)
68 cd01057 AAMH_A Aromatic and Al 20.9 86 0.0019 25.0 2.3 33 35-67 382-423 (465)
69 cd00173 SH2 Src homology 2 dom 20.3 1.3E+02 0.0029 17.3 2.7 43 32-74 35-82 (94)
70 cd01372 KISc_KIF4 Kinesin moto 20.2 1.6E+02 0.0035 21.7 3.6 22 36-57 68-91 (341)
No 1
>cd00265 MADS_MEF2_like MEF2 (myocyte enhancer factor 2)-like/Type II subfamily of MADS ( MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero and homo-dimers. Differs from SRF-like/Type I subgroup mainly in position of the alpha helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=100.00 E-value=7e-35 Score=178.67 Aligned_cols=77 Identities=57% Similarity=0.748 Sum_probs=74.4
Q ss_pred CcccceeEEecCCCccccccccccchhhhhhHhhhhhcccceeEEEecCCCceeecCCccHHHHHHHHhcCcCcchh
Q 040972 2 AREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSSSFITLWFHKSSHITSFLE 78 (87)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KRk~gL~KKa~ELs~LC~~~v~liv~~~~g~~~~~~s~~~~~vl~~y~~~~~~~~~ 78 (87)
||+||+|++|+|+.+|++||+||+.||||||.|||+||||+||+|||+|+|+++.|++|++++||++|++.+....|
T Consensus 1 gr~ki~i~~i~~~~~r~~tf~kR~~gl~kKa~Els~Lc~~~v~lvv~sp~gk~~~f~s~s~~~vl~ry~~~~~~~~~ 77 (77)
T cd00265 1 GRGKIEIKRIENSTNRQVTFSKRRNGLLKKAHELSVLCDAEVALIIFSSSGKLYEFSSPSMEKIIERYQKTSGSSLW 77 (77)
T ss_pred CCCcceeEEecCccHHHHHHHHhhhhhhhcceeheeccCCceeEEEEcCCCceEEecCCCHHHHHHHHHhccccccC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999887654
No 2
>KOG0014 consensus MADS box transcription factor [Transcription]
Probab=100.00 E-value=1.5e-34 Score=199.07 Aligned_cols=85 Identities=49% Similarity=0.655 Sum_probs=79.0
Q ss_pred CCcccceeEEecCCCccccccccccchhhhhhHhhhhhcccceeEEEecCCCceeecCCcc--HHHHHHHHhcCcCcchh
Q 040972 1 MAREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSSS--FITLWFHKSSHITSFLE 78 (87)
Q Consensus 1 MgR~ki~ik~I~~~~~R~~tf~KRk~gL~KKa~ELs~LC~~~v~liv~~~~g~~~~~~s~~--~~~vl~~y~~~~~~~~~ 78 (87)
|||+||+|++|+|++.|++||+||+.||||||+||||||||+||+|||||+|++|.|++++ +.+++++|.+.+.....
T Consensus 1 M~R~ki~i~~Ien~~~RqvTFsKRr~GL~KKA~ELsvLCd~eiavIifsp~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~ 80 (195)
T KOG0014|consen 1 MGRGKIEIKRIENESSRQVTFSKRRNGLFKKASELSVLCDAEIAVIVFSPSGKLYEFGSSDESVDAVVDRFLNLTEPSRK 80 (195)
T ss_pred CCCCccceeeccccchhhhhhHHHHhhHHHHHHHHHHhcCCeEEEEEECCCCCccccCCcchhHHHHHHHHHhhhhhhhc
Confidence 9999999999999999999999999999999999999999999999999999999998876 99999999998887776
Q ss_pred hhhhhhh
Q 040972 79 SKMKVKK 85 (87)
Q Consensus 79 kkm~~~~ 85 (87)
+++..++
T Consensus 81 ~~~~~~~ 87 (195)
T KOG0014|consen 81 KKRVNLE 87 (195)
T ss_pred ccccchh
Confidence 6665544
No 3
>cd00266 MADS_SRF_like SRF-like/Type I subfamily of MADS (MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero- and homo-dimers. Differs from the MEF-like/Type II subgroup mainly in position of the alpha 2 helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=99.97 E-value=3e-32 Score=169.01 Aligned_cols=81 Identities=47% Similarity=0.601 Sum_probs=75.5
Q ss_pred CcccceeEEecCCCccccccccccchhhhhhHhhhhhcccceeEEEecCCCceeecCCcc-HHHHHHHHhcCcCcchhhh
Q 040972 2 AREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSSS-FITLWFHKSSHITSFLESK 80 (87)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KRk~gL~KKa~ELs~LC~~~v~liv~~~~g~~~~~~s~~-~~~vl~~y~~~~~~~~~kk 80 (87)
||+||+|++|+|+.+|++||+||+.||+|||+|||+||||+||+|||+|+|+.+.|++++ +.++|++|...+...+.++
T Consensus 1 gr~Ki~i~~I~~~~~R~~tf~KRk~gl~kKa~ELs~Lc~~~v~~iv~sp~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 80 (83)
T cd00266 1 GRKKIKIKRIENKKKRAVTFSKRRQGLFKKASELSTLCGAEVAVIVYSPSGKLYVFWPSSEVEGVISRFEVLSALERKKK 80 (83)
T ss_pred CCccceeEEeeccchhhhhHHHhhhhHHHHHHHHHHhhCCcEEEEEECCCCCcceecCcHHHHHHHHHHhhcCHhhhhcc
Confidence 899999999999999999999999999999999999999999999999999999887755 9999999999998877766
Q ss_pred hh
Q 040972 81 MK 82 (87)
Q Consensus 81 m~ 82 (87)
+.
T Consensus 81 ~~ 82 (83)
T cd00266 81 AV 82 (83)
T ss_pred CC
Confidence 53
No 4
>smart00432 MADS MADS domain.
Probab=99.96 E-value=3.2e-30 Score=151.24 Aligned_cols=59 Identities=69% Similarity=1.037 Sum_probs=57.5
Q ss_pred CcccceeEEecCCCccccccccccchhhhhhHhhhhhcccceeEEEecCCCceeecCCc
Q 040972 2 AREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSS 60 (87)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KRk~gL~KKa~ELs~LC~~~v~liv~~~~g~~~~~~s~ 60 (87)
||+||+|++|+|+..|++||+||+.||+|||+|||+||||+||+|||+|+|+++.|++|
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 89999999999999999999999999999999999999999999999999999998875
No 5
>cd00120 MADS MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators. Binds DNA and exists as hetero and homo-dimers. Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ Type II. These subgroups differ mainly in position of the alpha 2 helix responsible for the dimerization interface; Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=99.95 E-value=1.6e-29 Score=148.19 Aligned_cols=59 Identities=71% Similarity=1.026 Sum_probs=57.3
Q ss_pred CcccceeEEecCCCccccccccccchhhhhhHhhhhhcccceeEEEecCCCceeecCCc
Q 040972 2 AREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSS 60 (87)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KRk~gL~KKa~ELs~LC~~~v~liv~~~~g~~~~~~s~ 60 (87)
||+||+|++|+|+..|++||+||+.||+|||+|||+|||++||+|||+|+|++++|+++
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 89999999999999999999999999999999999999999999999999999998864
No 6
>PF00319 SRF-TF: SRF-type transcription factor (DNA-binding and dimerisation domain); InterPro: IPR002100 Human serum response factor (SRF) is a ubiquitous nuclear protein important for cell proliferation and differentiation. SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as c-fos oncogene and muscle-specific actin genes. A core domain of around 90 amino acids is sufficient for the activities of DNA-binding, dimerisation and interaction with accessory factors. Within the core is a DNA-binding region, designated the MADS box [], that is highly similar to many eukaryotic regulatory proteins: among these are MCM1, the regulator of cell type-specific genes in fission yeast; DSRF, a Drosophila trachea development factor; the MEF2 family of myocyte-specific enhancer factors; and the Agamous and Deficiens families of plant homeotic proteins. In SRF, the MADS box has been shown to be involved in DNA-binding and dimerisation []. Proteins belonging to the MADS family function as dimers, the primary DNA-binding element of which is an anti-parallel coiled coil of two amphipathic alpha-helices, one from each subunit. The DNA wraps around the coiled coil allowing the basic N-termini of the helices to fit into the DNA major groove. The chain extending from the helix N-termini reaches over the DNA backbone and penetrates into the minor groove. A 4-stranded, anti-parallel beta-sheet packs against the coiled-coil face opposite the DNA and is the central element of the dimerisation interface. The MADS-box domain is commonly found associated with K-box region see IPR002487 from INTERPRO ; GO: 0003677 DNA binding, 0046983 protein dimerization activity; PDB: 1MNM_B 1N6J_A 1TQE_S 3MU6_D 3P57_I 1EGW_A 1C7U_B 3KOV_A 1HBX_A 1K6O_C ....
Probab=99.93 E-value=1e-27 Score=136.95 Aligned_cols=51 Identities=55% Similarity=0.947 Sum_probs=46.8
Q ss_pred EEecCCCccccccccccchhhhhhHhhhhhcccceeEEEecCCCceeecCC
Q 040972 9 RKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSS 59 (87)
Q Consensus 9 k~I~~~~~R~~tf~KRk~gL~KKa~ELs~LC~~~v~liv~~~~g~~~~~~s 59 (87)
++|+|+..|++||+||+.||+|||+|||+||||+||+|||+|+|++++|+|
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 579999999999999999999999999999999999999999999999986
No 7
>KOG0015 consensus Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.83 E-value=1e-21 Score=144.98 Aligned_cols=65 Identities=38% Similarity=0.545 Sum_probs=61.3
Q ss_pred CcccceeEEecCCCccccccccccchhhhhhHhhhhhcccceeEEEecCCCceeecCCccHHHHH
Q 040972 2 AREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSSSFITLW 66 (87)
Q Consensus 2 gR~ki~ik~I~~~~~R~~tf~KRk~gL~KKa~ELs~LC~~~v~liv~~~~g~~~~~~s~~~~~vl 66 (87)
||+||+|++|+|+..|.+||+|||.||||||+||++|+|.+|.|+|.+++|.+|+|..|.++.||
T Consensus 63 gr~kik~eyIenK~rR~~tFSKRK~GImKKAyELs~LTGtqVllLVaSEtGhVyTFaTpKLep~i 127 (338)
T KOG0015|consen 63 GRVKIKMEYIENKLRRYVTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATPKLEPMI 127 (338)
T ss_pred ceeeccchhhcccceeeeeehhhhhhhHHHHHHhhhcccceEEEEEEecCcceEEeccccccccc
Confidence 79999999999999999999999999999999999999999999999999999999987665544
No 8
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=99.55 E-value=1.7e-15 Score=115.62 Aligned_cols=68 Identities=38% Similarity=0.463 Sum_probs=64.0
Q ss_pred CCcccceeEEecCCCccccccccccchhhhhhHhhhhhcccceeEEEecCCCceeecCCccHHHHHHH
Q 040972 1 MAREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSSSSFITLWFH 68 (87)
Q Consensus 1 MgR~ki~ik~I~~~~~R~~tf~KRk~gL~KKa~ELs~LC~~~v~liv~~~~g~~~~~~s~~~~~vl~~ 68 (87)
|||++|.|.+|+|+.+|.+||+||+.||+|||.||++|.|.+|.++|.+.+|.++.|+.|..+.|+..
T Consensus 81 ~~~~~~~is~i~nk~~r~vtf~Krk~gI~kka~ElsvLt~~~vl~lvise~g~v~tf~tp~~e~v~~~ 148 (412)
T COG5068 81 VTGRKIGISYITNKTKRSVTFSKRKHGINKKAFELSVLTGTEVLLLVISENGLVHTFTTPKLESVVKS 148 (412)
T ss_pred cccccCCcccccCcccccchhhhhhhhhhhhhhhhhhccCCceEEEEecCCCceeeecCCcccccccc
Confidence 78999999999999999999999999999999999999999999999999999999998877776543
No 9
>PF10491 Nrf1_DNA-bind: NLS-binding and DNA-binding and dimerisation domains of Nrf1; InterPro: IPR019525 Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates. The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila []. In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human []. The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein, Q8C4C0 from SWISSPROT, there is also an NLS domain at 88-116, and a DNA binding and dimerisation domain at 127-282. Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity [].
Probab=76.73 E-value=3.7 Score=29.62 Aligned_cols=48 Identities=10% Similarity=0.090 Sum_probs=37.6
Q ss_pred chhhhhh----HhhhhhcccceeEEEecCCC---ceeecCCccHHHHHHHHhcCc
Q 040972 26 RGLFKKA----EELSVLCDAEVGVIIFSATG---KLFESSSSSFITLWFHKSSHI 73 (87)
Q Consensus 26 ~gL~KKa----~ELs~LC~~~v~liv~~~~g---~~~~~~s~~~~~vl~~y~~~~ 73 (87)
.-|+.|. .|+++-+|-+++|++++|+. ....|+...+++|+..|...-
T Consensus 35 ~rllrkl~~~~de~~trvGqqavvl~~~p~kp~~~f~vfGa~pL~~vv~~~~~~I 89 (214)
T PF10491_consen 35 TRLLRKLRQTIDEYTTRVGQQAVVLCCTPSKPNPVFKVFGAAPLENVVRNLKPVI 89 (214)
T ss_pred HHHHHHHHHHHHHHHHhhhceeEEEEecCCCCCCceeeecchhHHHHHHHHHHHH
Confidence 4456654 79999999999999999853 244688888999999887643
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=73.20 E-value=4.4 Score=20.92 Aligned_cols=24 Identities=17% Similarity=0.246 Sum_probs=16.7
Q ss_pred hhhhhcccceeEEEecCCCceeec
Q 040972 34 ELSVLCDAEVGVIIFSATGKLFES 57 (87)
Q Consensus 34 ELs~LC~~~v~liv~~~~g~~~~~ 57 (87)
.|+--||+-|.+.||+..|..-.|
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 467789999999999999975443
No 11
>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=61.44 E-value=1.2 Score=21.22 Aligned_cols=13 Identities=38% Similarity=0.866 Sum_probs=9.6
Q ss_pred eEEEecCCCceee
Q 040972 44 GVIIFSATGKLFE 56 (87)
Q Consensus 44 ~liv~~~~g~~~~ 56 (87)
.+.+|||+|+++.
T Consensus 4 ~~t~FSp~Grl~Q 16 (23)
T PF10584_consen 4 SITTFSPDGRLFQ 16 (23)
T ss_dssp STTSBBTTSSBHH
T ss_pred CceeECCCCeEEe
Confidence 4557999998763
No 12
>KOG4637 consensus Adaptor for phosphoinositide 3-kinase [Signal transduction mechanisms]
Probab=55.59 E-value=8.3 Score=30.41 Aligned_cols=47 Identities=30% Similarity=0.254 Sum_probs=32.0
Q ss_pred Hhhhhhcccce--eEEEecCCCceeecCC---ccHHHHHHHHhcCcCcchhh
Q 040972 33 EELSVLCDAEV--GVIIFSATGKLFESSS---SSFITLWFHKSSHITSFLES 79 (87)
Q Consensus 33 ~ELs~LC~~~v--~liv~~~~g~~~~~~s---~~~~~vl~~y~~~~~~~~~k 79 (87)
+-||++||-+| |||--...|=.|.-|- .++.+++.+|+..|-...-+
T Consensus 367 yalSV~~~~~V~HClIy~tatG~GFa~pyn~y~tlk~lV~hY~h~SLe~HnD 418 (464)
T KOG4637|consen 367 YALSVVHDGEVKHCLIYQTATGFGFAEPYNLYSTLKELVLHYQHTSLEQHND 418 (464)
T ss_pred eEEEEEECCceeeeEEeeccccccccchhHHHHHHHHHHHHHhhhhHHhhcc
Confidence 57999999887 6655444553333222 68999999999887655433
No 13
>PF09941 DUF2173: Uncharacterized conserved protein (DUF2173); InterPro: IPR018685 This family of various hypothetical prokaryotic proteins has no known function.
Probab=52.66 E-value=27 Score=22.59 Aligned_cols=37 Identities=22% Similarity=0.190 Sum_probs=25.5
Q ss_pred hHhhhhhcccceeEEEecCCCceeecCC---ccHHHHHHHH
Q 040972 32 AEELSVLCDAEVGVIIFSATGKLFESSS---SSFITLWFHK 69 (87)
Q Consensus 32 a~ELs~LC~~~v~liv~~~~g~~~~~~s---~~~~~vl~~y 69 (87)
-.+|..|-||-+ ...|+++|++.+|-. +..-+++.++
T Consensus 3 l~~Lm~lpGv~A-Ag~Fs~~G~l~e~~G~l~~~~a~m~A~m 42 (108)
T PF09941_consen 3 LDKLMKLPGVVA-AGEFSDDGKLVEYKGELDEEMAEMLAKM 42 (108)
T ss_pred HHHhhcCCCeEE-EEEECCCCeEEeeecCCCHHHHHHHHHH
Confidence 467888888855 467999999988765 3444444443
No 14
>TIGR01916 F420_cofE F420-0:gamma-glutamyl ligase. This model represents an enzyme of coenzyme F(420) biosynthesis, as catalyzed by MJ0768 of Methanococcus jannaschii and by the N-terminal half of FbiB of Mycobacterium bovis strain BCG. Note that only two glutamates are ligated in M. jannaschii, but five to six in the Mycobacterium lineage. In M. jannaschii, CofE catalyzes the GTP-dependent addition of two L-glutamates.
Probab=50.10 E-value=15 Score=27.04 Aligned_cols=27 Identities=33% Similarity=0.543 Sum_probs=22.4
Q ss_pred HhhhhhcccceeEEEecCCCceeecCC
Q 040972 33 EELSVLCDAEVGVIIFSATGKLFESSS 59 (87)
Q Consensus 33 ~ELs~LC~~~v~liv~~~~g~~~~~~s 59 (87)
.+|.-.+|++|++||.++.|.+|.-+.
T Consensus 133 ~~l~~~~g~~v~VIItDt~gr~~R~G~ 159 (243)
T TIGR01916 133 RGLRELTGVDVGVIITDTNGRPFREGQ 159 (243)
T ss_pred HHHHHHHCCCEEEEEECCCCCccccCC
Confidence 457778999999999999998876554
No 15
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=47.58 E-value=11 Score=24.33 Aligned_cols=68 Identities=21% Similarity=0.192 Sum_probs=36.6
Q ss_pred CCcccceeEEecCCCccccccccccchhhhhhHhhhhhccc----ceeEEEecCCCceeecCC-------ccHHHHHHHH
Q 040972 1 MAREKIKIRKIDNITARQVTFSKRRRGLFKKAEELSVLCDA----EVGVIIFSATGKLFESSS-------SSFITLWFHK 69 (87)
Q Consensus 1 MgR~ki~ik~I~~~~~R~~tf~KRk~gL~KKa~ELs~LC~~----~v~liv~~~~g~~~~~~s-------~~~~~vl~~y 69 (87)
|||++.+.+.|-. .|+..+.|+-..++ =-+|.++.|-+ .+++++.+..|.-+..-- .--..+++-|
T Consensus 1 MG~rr~krr~~ik--~~~~~L~k~FtCp~-Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~l~~~vDvYs~wvDay 77 (104)
T COG4888 1 MGRRRRKRRKIIK--RRPQVLPKTFTCPR-CGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPELSEPVDVYSAWVDAY 77 (104)
T ss_pred CCcccccccccCc--ccCccCCceEecCc-cCCeeeeEEEEEecCceeEEEcccCcceEEEeccccccchhHHHHHHHHH
Confidence 9999988887754 22322444433332 11444454544 346677777776554322 2344566666
Q ss_pred hc
Q 040972 70 SS 71 (87)
Q Consensus 70 ~~ 71 (87)
..
T Consensus 78 ~e 79 (104)
T COG4888 78 LE 79 (104)
T ss_pred Hh
Confidence 54
No 16
>PF14263 DUF4354: Domain of unknown function (DUF4354); PDB: 3NRF_B 3SB3_A.
Probab=46.15 E-value=7.4 Score=25.84 Aligned_cols=42 Identities=26% Similarity=0.354 Sum_probs=29.6
Q ss_pred ecCCCccccccccccchhhhhhHhhhhhcccceeEEEecCCCceeec
Q 040972 11 IDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFES 57 (87)
Q Consensus 11 I~~~~~R~~tf~KRk~gL~KKa~ELs~LC~~~v~liv~~~~g~~~~~ 57 (87)
+.++.....||.-.-..|..+.-+|+.+| ++.|+|.|+-+..
T Consensus 41 v~~k~~ytktF~V~vaN~s~~~idLsk~C-----f~a~~~~gk~f~l 82 (124)
T PF14263_consen 41 VGGKSFYTKTFDVTVANLSDKDIDLSKMC-----FKAYSPDGKEFKL 82 (124)
T ss_dssp ETTEEEEEEEEEEEEEE-SSS-EE-TT-E-----EEEEETTS-EEEE
T ss_pred ecCccceEEEEEEEEecCCCCccccccch-----hhhccccCCEEEe
Confidence 45666777788888888889999999986 9999999986653
No 17
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=44.84 E-value=24 Score=23.64 Aligned_cols=46 Identities=9% Similarity=0.081 Sum_probs=29.8
Q ss_pred hhhhhcccce----eEEEecCCCceeecCCccHHHHHHHHhcCcCcchhhh
Q 040972 34 ELSVLCDAEV----GVIIFSATGKLFESSSSSFITLWFHKSSHITSFLESK 80 (87)
Q Consensus 34 ELs~LC~~~v----~liv~~~~g~~~~~~s~~~~~vl~~y~~~~~~~~~kk 80 (87)
++|..||..| ....+-.+|+++.|+++....... ....|....|-+
T Consensus 5 e~CsFcG~kIyPG~G~~fVR~DGkvf~FcssKC~k~f~-~kRnPRKlkWT~ 54 (131)
T PRK14891 5 RTCDYTGEEIEPGTGTMFVRKDGTVLHFVDSKCEKNYD-LGREARDLEWTE 54 (131)
T ss_pred eeecCcCCcccCCCCcEEEecCCCEEEEecHHHHHHHH-ccCCCccchhHH
Confidence 5678888887 334445579999999976654432 344555555544
No 18
>PRK13293 F420-0--gamma-glutamyl ligase; Reviewed
Probab=43.42 E-value=22 Score=26.10 Aligned_cols=27 Identities=37% Similarity=0.561 Sum_probs=22.2
Q ss_pred HhhhhhcccceeEEEecCCCceeecCC
Q 040972 33 EELSVLCDAEVGVIIFSATGKLFESSS 59 (87)
Q Consensus 33 ~ELs~LC~~~v~liv~~~~g~~~~~~s 59 (87)
.+|.-.+|++|++||.+..|.+|-.+.
T Consensus 134 ~~l~~~~g~~v~VIItDt~gr~~R~G~ 160 (245)
T PRK13293 134 EGLEELTGKKVGVIITDTNGRPFRKGQ 160 (245)
T ss_pred HHHHHHHCCCEEEEEEcCCCcccccCC
Confidence 357778999999999999998877654
No 19
>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=41.47 E-value=37 Score=23.27 Aligned_cols=23 Identities=22% Similarity=0.368 Sum_probs=16.6
Q ss_pred hhcccceeEEEecCCCceee-cCC
Q 040972 37 VLCDAEVGVIIFSATGKLFE-SSS 59 (87)
Q Consensus 37 ~LC~~~v~liv~~~~g~~~~-~~s 59 (87)
.-|++.|-+++|||+.+.|. |-+
T Consensus 109 p~c~iKvL~LlYs~kk~~flG~IP 132 (152)
T PF11232_consen 109 PPCEIKVLMLLYSPKKKAFLGFIP 132 (152)
T ss_dssp SSSS-SEEEEEEETTTTEEEEEEE
T ss_pred CCCceEEEEEEEcCCCceEEEEcC
Confidence 45888999999999888553 443
No 20
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=41.08 E-value=49 Score=19.66 Aligned_cols=44 Identities=16% Similarity=0.323 Sum_probs=29.0
Q ss_pred hhhhcccce----eEEEecCCCceeecCCccHHHHHHHHhcCcCcchhh
Q 040972 35 LSVLCDAEV----GVIIFSATGKLFESSSSSFITLWFHKSSHITSFLES 79 (87)
Q Consensus 35 Ls~LC~~~v----~liv~~~~g~~~~~~s~~~~~vl~~y~~~~~~~~~k 79 (87)
-|..||.++ .++.+-.+|.++.|+|+.-.. +-.+...|....|-
T Consensus 5 ~CsFcG~~I~PGtG~m~Vr~Dg~v~~FcssKc~k-~~~~~rnPRk~~WT 52 (66)
T COG2075 5 VCSFCGKKIEPGTGIMYVRNDGKVLRFCSSKCEK-LFKLGRNPRKLKWT 52 (66)
T ss_pred EecCcCCccCCCceEEEEecCCeEEEEechhHHH-HHHccCCCccchhH
Confidence 355688776 455556689999999977776 44455555554443
No 21
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=40.69 E-value=30 Score=29.05 Aligned_cols=23 Identities=30% Similarity=0.410 Sum_probs=20.8
Q ss_pred hhhcccceeEEEecCCCceeecC
Q 040972 36 SVLCDAEVGVIIFSATGKLFESS 58 (87)
Q Consensus 36 s~LC~~~v~liv~~~~g~~~~~~ 58 (87)
|+|.|+-++||.++++|.++.+.
T Consensus 374 ~VLsgvtaGVi~~d~~g~i~t~N 396 (712)
T COG5000 374 AVLSGLTAGVIGFDNRGCITTVN 396 (712)
T ss_pred HHHhcCceeEEEEcCCCeeEeec
Confidence 69999999999999999988755
No 22
>PF14009 DUF4228: Domain of unknown function (DUF4228)
Probab=38.09 E-value=49 Score=21.46 Aligned_cols=34 Identities=15% Similarity=0.216 Sum_probs=24.4
Q ss_pred cccceeEEEecCCCceeecCC-ccHHHHHHHHhcC
Q 040972 39 CDAEVGVIIFSATGKLFESSS-SSFITLWFHKSSH 72 (87)
Q Consensus 39 C~~~v~liv~~~~g~~~~~~s-~~~~~vl~~y~~~ 72 (87)
++...++-|..++|.+..|.. -.+.+|+..|=.+
T Consensus 12 ~~~~~~vkvv~~~G~v~~~~~pv~a~evm~~~P~h 46 (181)
T PF14009_consen 12 SSSAATVKVVHPDGKVEEFKRPVTAAEVMLENPGH 46 (181)
T ss_pred cCCCceEEEEcCCCcEEEeCCCcCHHHHHHHCCCC
Confidence 344555555568999998877 5899999887544
No 23
>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=36.05 E-value=1.1e+02 Score=19.00 Aligned_cols=56 Identities=21% Similarity=0.269 Sum_probs=37.3
Q ss_pred Ccccccccc--ccchhhhhhHhhhhhcccceeEEEecCCCceeecCC-ccHHHHHHHHh
Q 040972 15 TARQVTFSK--RRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSS-SSFITLWFHKS 70 (87)
Q Consensus 15 ~~R~~tf~K--Rk~gL~KKa~ELs~LC~~~v~liv~~~~g~~~~~~s-~~~~~vl~~y~ 70 (87)
..|+..|.. -..+|..|..+|--|....++|--.+.+|+..+-++ .+++++.....
T Consensus 10 ~~RRf~~~~~pt~~~L~~kl~~Lf~lp~~~~~vtYiDeD~D~ITlssd~eL~d~~~~~~ 68 (82)
T cd06397 10 DTRRIVFPDIPTWEALASKLENLYNLPEIKVGVTYIDNDNDEITLSSNKELQDFYRLSH 68 (82)
T ss_pred ceEEEecCCCccHHHHHHHHHHHhCCChhHeEEEEEcCCCCEEEecchHHHHHHHHhcc
Confidence 344444433 236888888888888876666555677888888777 56776665433
No 24
>COG0139 HisI Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]
Probab=35.56 E-value=11 Score=24.69 Aligned_cols=27 Identities=22% Similarity=0.457 Sum_probs=21.9
Q ss_pred hhhhhhHhhhhhcccceeEEEecCCCc
Q 040972 27 GLFKKAEELSVLCDAEVGVIIFSATGK 53 (87)
Q Consensus 27 gL~KKa~ELs~LC~~~v~liv~~~~g~ 53 (87)
|=+.|+.|+.+-||.|+.++++.+.|.
T Consensus 69 G~~q~v~~i~~DCD~Dall~~V~q~gg 95 (111)
T COG0139 69 GHTQKVVEIRLDCDGDALLLLVEQIGG 95 (111)
T ss_pred CceEEEEEEEcCCCCCEEEEEEEeCCC
Confidence 445567889999999999999988553
No 25
>PRK09555 feoA ferrous iron transport protein A; Reviewed
Probab=34.27 E-value=59 Score=19.23 Aligned_cols=32 Identities=16% Similarity=0.156 Sum_probs=27.7
Q ss_pred chhhhhhHhhhhhcccceeEEEecCCCceeec
Q 040972 26 RGLFKKAEELSVLCDAEVGVIIFSATGKLFES 57 (87)
Q Consensus 26 ~gL~KKa~ELs~LC~~~v~liv~~~~g~~~~~ 57 (87)
..+..+-.+|-++.|++|-++-..|-|.+..+
T Consensus 20 ~~~~~rL~~mGl~pG~~V~v~~~aP~gdPi~i 51 (74)
T PRK09555 20 PAYRQKLLSLGMLPGSSFNVVRVAPLGDPIHI 51 (74)
T ss_pred hHHHHHHHHcCCCCCCEEEEEEECCCCCCEEE
Confidence 45788999999999999999999998876654
No 26
>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=33.40 E-value=60 Score=19.38 Aligned_cols=33 Identities=24% Similarity=0.336 Sum_probs=21.1
Q ss_pred hhhhhcccce----eEEEecCCCceeecCCccHHHHH
Q 040972 34 ELSVLCDAEV----GVIIFSATGKLFESSSSSFITLW 66 (87)
Q Consensus 34 ELs~LC~~~v----~liv~~~~g~~~~~~s~~~~~vl 66 (87)
|+|..||-+| ..+.+-.||+++.|.+.......
T Consensus 4 ~~C~Fsg~~I~PG~G~~~Vr~DG~v~~F~s~Kc~~~~ 40 (71)
T PF01246_consen 4 EKCSFSGYKIYPGHGKMYVRNDGKVFYFCSSKCEKLF 40 (71)
T ss_dssp EE-TTT-SEE-SSSSEEEE-TTS-EEEESSHHHHHHH
T ss_pred EEecccCCccCCCCCeEEEecCCCeEEEeCHHHHHHH
Confidence 5677888877 34555678999999997666654
No 27
>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=31.38 E-value=66 Score=16.96 Aligned_cols=26 Identities=15% Similarity=0.254 Sum_probs=15.9
Q ss_pred cccce---eEEEecCCCceeecCCccHHH
Q 040972 39 CDAEV---GVIIFSATGKLFESSSSSFIT 64 (87)
Q Consensus 39 C~~~v---~liv~~~~g~~~~~~s~~~~~ 64 (87)
||..| +-.-..-+|+.|.|+|+.-.+
T Consensus 6 cg~~v~~~~~~~~~y~G~~Y~FCS~~C~~ 34 (47)
T PF04945_consen 6 CGMKVPGNAAYSVEYNGRTYYFCSEGCKE 34 (47)
T ss_dssp GG-BE-----EEEEETTEEEEESSHHHHH
T ss_pred CCCEEccCccEEEEECCEEEEEcCHHHHH
Confidence 56666 444445579999999965544
No 28
>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=31.31 E-value=46 Score=24.96 Aligned_cols=24 Identities=17% Similarity=0.261 Sum_probs=19.2
Q ss_pred hhhcccceeEEEecCC--Cceee-cCC
Q 040972 36 SVLCDAEVGVIIFSAT--GKLFE-SSS 59 (87)
Q Consensus 36 s~LC~~~v~liv~~~~--g~~~~-~~s 59 (87)
+++-|.+++++.|++. ||.|+ |+.
T Consensus 83 ~~l~G~n~~i~ayGqtGSGKT~Tm~G~ 109 (356)
T cd01365 83 HAFEGYNVCLFAYGQTGSGKSYTMMGY 109 (356)
T ss_pred HHhCCCceEEEEecCCCCCCeEEecCC
Confidence 4789999999999884 67776 554
No 29
>PF13540 RCC1_2: Regulator of chromosome condensation (RCC1) repeat; PDB: 3QI0_D 1JTD_B 3QHY_B.
Probab=30.68 E-value=38 Score=16.32 Aligned_cols=22 Identities=14% Similarity=0.297 Sum_probs=15.2
Q ss_pred hhcccceeEEEecCCCceeecCC
Q 040972 37 VLCDAEVGVIIFSATGKLFESSS 59 (87)
Q Consensus 37 ~LC~~~v~liv~~~~g~~~~~~s 59 (87)
+-||..-.+++.+ +|.++.|+.
T Consensus 4 ia~G~~ht~al~~-~g~v~~wG~ 25 (30)
T PF13540_consen 4 IACGGYHTCALTS-DGEVYCWGD 25 (30)
T ss_dssp EEEESSEEEEEE--TTEEEEEE-
T ss_pred EEecCCEEEEEEc-CCCEEEEcC
Confidence 4577777777665 689999875
No 30
>PRK09822 lipopolysaccharide core biosynthesis protein; Provisional
Probab=30.22 E-value=30 Score=25.67 Aligned_cols=41 Identities=17% Similarity=0.368 Sum_probs=27.7
Q ss_pred ccccccccchhhhhhHhhhhhcccceeE---EEecCCCceeecCC
Q 040972 18 QVTFSKRRRGLFKKAEELSVLCDAEVGV---IIFSATGKLFESSS 59 (87)
Q Consensus 18 ~~tf~KRk~gL~KKa~ELs~LC~~~v~l---iv~~~~g~~~~~~s 59 (87)
+.-|.+-+.|++||. .+..||+.+-++ |.+|+.+..+.|+.
T Consensus 117 ~~~~~~~~~~~~~~~-~~~~L~~~~~~l~~~v~fS~~~r~IGFSk 160 (269)
T PRK09822 117 RSFYRREKGGFLKKI-KFNILKRVHKALLISVPLSKRGRLAGFCK 160 (269)
T ss_pred hhhhhhccCchhhhh-HHHHHhhhhhhhEEEeeccccCCceeeee
Confidence 344566678888876 477788876655 44788777666654
No 31
>COG4917 EutP Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=29.62 E-value=42 Score=22.88 Aligned_cols=24 Identities=21% Similarity=0.178 Sum_probs=17.5
Q ss_pred hhhhhcccceeEEEecCCCceeec
Q 040972 34 ELSVLCDAEVGVIIFSATGKLFES 57 (87)
Q Consensus 34 ELs~LC~~~v~liv~~~~g~~~~~ 57 (87)
=+.++||++|-++|-+-+.+...|
T Consensus 58 L~tt~~dadvi~~v~~and~~s~f 81 (148)
T COG4917 58 LITTLQDADVIIYVHAANDPESRF 81 (148)
T ss_pred HHHHhhccceeeeeecccCccccC
Confidence 367899999998887766553333
No 32
>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=29.39 E-value=53 Score=18.56 Aligned_cols=33 Identities=24% Similarity=0.411 Sum_probs=22.0
Q ss_pred hhhhhcccce----eEEEecCCCceeecCCccHHHHH
Q 040972 34 ELSVLCDAEV----GVIIFSATGKLFESSSSSFITLW 66 (87)
Q Consensus 34 ELs~LC~~~v----~liv~~~~g~~~~~~s~~~~~vl 66 (87)
|+|..||-+| ....+..||+++.|.+...+...
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~F~s~Kc~~~~ 40 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFRFCSSKCEKNF 40 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEEEECHHHHHHH
Confidence 5677777776 23444558999999996655443
No 33
>PF00383 dCMP_cyt_deam_1: Cytidine and deoxycytidylate deaminase zinc-binding region; InterPro: IPR002125 Cytidine deaminase (3.5.4.5 from EC) (cytidine aminohydrolase) catalyzes the hydrolysis of cytidine into uridine and ammonia while deoxycytidylate deaminase (3.5.4.12 from EC) (dCMP deaminase) hydrolyzes dCMP into dUMP. Both enzymes are known to bind zinc and to require it for their catalytic activity [, ]. These two enzymes do not share any sequence similarity with the exception of a region that contains three conserved histidine and cysteine residues which are thought to be involved in the binding of the catalytic zinc ion. Such a region is also found in other proteins [, ]: Yeast cytosine deaminase (3.5.4.1 from EC) (gene FCY1) which transforms cytosine into uracil. Mammalian apolipoprotein B mRNA editing protein, responsible for the postranscriptional editing of a CAA codon into a UAA (stop) codon in the APOB mRNA. Riboflavin biosynthesis protein ribG, which converts 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1H,3H)-pyrimidinedione 5'-phosphate. Bacillus cereus blasticidin-S deaminase (3.5.4.23 from EC), which catalyzes the deamination of the cytosine moiety of the antibiotics blasticidin S, cytomycin and acetylblasticidin S. Bacillus subtilis protein comEB. This protein is required for the binding and uptake of transforming DNA. B. subtilis hypothetical protein yaaJ. Escherichia coli hypothetical protein yfhC. Yeast hypothetical protein YJL035c. ; GO: 0008270 zinc ion binding, 0016787 hydrolase activity; PDB: 3MPZ_C 3R2N_C 1WKQ_A 1TIY_B 2B3J_C 2O7P_B 2OBC_A 2G6V_B 2D30_B 2D5N_B ....
Probab=29.37 E-value=83 Score=18.70 Aligned_cols=28 Identities=29% Similarity=0.455 Sum_probs=20.0
Q ss_pred hhhhhhHhhhhhc----ccceeEEEecCCCce
Q 040972 27 GLFKKAEELSVLC----DAEVGVIIFSATGKL 54 (87)
Q Consensus 27 gL~KKa~ELs~LC----~~~v~liv~~~~g~~ 54 (87)
-+++.|.+++... +..|+.++++++|+.
T Consensus 6 ~~m~~a~~~a~~s~~~~~~~vgaviv~~~~~~ 37 (102)
T PF00383_consen 6 EFMRIAIELAKRSRPCGNFPVGAVIVDPDGKI 37 (102)
T ss_dssp HHHHHHHHHHHTHBTTTSSSEEEEEEETTTEE
T ss_pred HHHHHHHHHHHhccccCCCCEEEEEEeccCcc
Confidence 3567777776666 778888888876553
No 34
>PF01996 F420_ligase: F420-0:Gamma-glutamyl ligase; InterPro: IPR002847 This entry contains F420-0:gamma-glutamyl ligase and related proteins. F420-0:gamma-glutamyl ligase catalyzes the GTP-dependent successive addition of multiple gamma-linked L-glutamates to the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) to form polyglutamated F420 derivatives [, , , ].; PDB: 2G9I_A 2PHN_A.
Probab=28.97 E-value=15 Score=26.33 Aligned_cols=27 Identities=33% Similarity=0.487 Sum_probs=18.8
Q ss_pred HhhhhhcccceeEEEecCCCceeecCC
Q 040972 33 EELSVLCDAEVGVIIFSATGKLFESSS 59 (87)
Q Consensus 33 ~ELs~LC~~~v~liv~~~~g~~~~~~s 59 (87)
.+|.-.+|++|++||.+++|.+|..++
T Consensus 141 ~~l~~~~g~~v~ViI~Dt~gr~~r~G~ 167 (228)
T PF01996_consen 141 EELKERTGKDVGVIITDTNGRPWRLGQ 167 (228)
T ss_dssp HHHHHHHS---EEEEEEEEEETTEECE
T ss_pred HHHHHHHCCceEEEEECCCCcEEecCC
Confidence 467788999999999998887665554
No 35
>KOG0183 consensus 20S proteasome, regulatory subunit alpha type PSMA7/PRE6 [Posttranslational modification, protein turnover, chaperones]
Probab=28.94 E-value=39 Score=24.82 Aligned_cols=19 Identities=26% Similarity=0.564 Sum_probs=14.7
Q ss_pred cceeEEEecCCCceee--cCC
Q 040972 41 AEVGVIIFSATGKLFE--SSS 59 (87)
Q Consensus 41 ~~v~liv~~~~g~~~~--~~s 59 (87)
-|-+|-||||+|.++. |.+
T Consensus 4 ydraltvFSPDGhL~QVEYAq 24 (249)
T KOG0183|consen 4 YDRALTVFSPDGHLFQVEYAQ 24 (249)
T ss_pred cccceEEECCCCCEEeeHhHH
Confidence 4678999999999864 543
No 36
>COG4831 Roadblock/LC7 domain [Function unknown]
Probab=28.81 E-value=81 Score=20.31 Aligned_cols=29 Identities=31% Similarity=0.313 Sum_probs=22.5
Q ss_pred hhhHhhhhhcccceeEEEecCCCceeecCC
Q 040972 30 KKAEELSVLCDAEVGVIIFSATGKLFESSS 59 (87)
Q Consensus 30 KKa~ELs~LC~~~v~liv~~~~g~~~~~~s 59 (87)
.|..||-.+-||-++ =.|||+|++..|-+
T Consensus 3 ekLdeLlqi~Gv~AA-Gefs~DGkLv~Ykg 31 (109)
T COG4831 3 EKLDELLQIKGVMAA-GEFSPDGKLVEYKG 31 (109)
T ss_pred hhHHHHhCccceeEe-ceeCCCCceEEeeC
Confidence 467788888887554 46899999999876
No 37
>COG3411 Ferredoxin [Energy production and conversion]
Probab=27.89 E-value=98 Score=18.26 Aligned_cols=28 Identities=7% Similarity=0.052 Sum_probs=19.7
Q ss_pred eEEEecCCCceeecCC-ccHHHHHHHHhc
Q 040972 44 GVIIFSATGKLFESSS-SSFITLWFHKSS 71 (87)
Q Consensus 44 ~liv~~~~g~~~~~~s-~~~~~vl~~y~~ 71 (87)
.++++.|+|-+|..-+ +.++.|++....
T Consensus 18 Pvl~vYpegvWY~~V~p~~a~rIv~~hl~ 46 (64)
T COG3411 18 PVLVVYPEGVWYTRVDPEDARRIVQSHLL 46 (64)
T ss_pred CEEEEecCCeeEeccCHHHHHHHHHHHHh
Confidence 3566667887776555 789999987654
No 38
>smart00252 SH2 Src homology 2 domains. Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae.
Probab=27.57 E-value=1e+02 Score=17.64 Aligned_cols=42 Identities=24% Similarity=0.201 Sum_probs=23.7
Q ss_pred Hhhhhhccccee-EEEe-cCCCceeecC---CccHHHHHHHHhcCcC
Q 040972 33 EELSVLCDAEVG-VIIF-SATGKLFESS---SSSFITLWFHKSSHIT 74 (87)
Q Consensus 33 ~ELs~LC~~~v~-liv~-~~~g~~~~~~---s~~~~~vl~~y~~~~~ 74 (87)
.-||+.++..+- ..|. .++|..+... -+++.++|+.|...+.
T Consensus 37 ~~Lsv~~~~~~~h~~I~~~~~~~~~l~~~~~F~sl~eLI~~y~~~~~ 83 (84)
T smart00252 37 YVLSVRVKGKVKHYRIRRNEDGKFYLDGGRKFPSLVELVEHYQKNSL 83 (84)
T ss_pred EEEEEEECCEEEEEEEEECCCCcEEECCCCccCCHHHHHHHHhhCCC
Confidence 346666665542 2333 3334333222 1799999999987663
No 39
>PRK13294 F420-0--gamma-glutamyl ligase; Provisional
Probab=26.94 E-value=52 Score=25.99 Aligned_cols=27 Identities=15% Similarity=0.319 Sum_probs=22.1
Q ss_pred HhhhhhcccceeEEEecCCCceeecCC
Q 040972 33 EELSVLCDAEVGVIIFSATGKLFESSS 59 (87)
Q Consensus 33 ~ELs~LC~~~v~liv~~~~g~~~~~~s 59 (87)
.+|.-.+|++|+|||.+..|.++--+.
T Consensus 134 ~~l~~~~g~~v~vii~Dt~gr~~r~g~ 160 (448)
T PRK13294 134 AGLRERLGVDVAVVVTDTMGRAWRNGQ 160 (448)
T ss_pred HHHHHHHCCCEEEEEecCCCCccccCc
Confidence 457788999999999999888776554
No 40
>PRK00807 50S ribosomal protein L24e; Validated
Probab=26.43 E-value=1.1e+02 Score=17.00 Aligned_cols=44 Identities=11% Similarity=0.117 Sum_probs=25.9
Q ss_pred hhhhhccccee----EEEecCCCceeecCCccHHHHHHHHhcCcCcchh
Q 040972 34 ELSVLCDAEVG----VIIFSATGKLFESSSSSFITLWFHKSSHITSFLE 78 (87)
Q Consensus 34 ELs~LC~~~v~----liv~~~~g~~~~~~s~~~~~vl~~y~~~~~~~~~ 78 (87)
+++.-||-+|- ...+-.+|+++.|.++...+.. .....|....|
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~Fcs~KC~~~f-~~~~nprk~~W 49 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILYFCSSKCEKNY-KLGRVPRKLKW 49 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEEEeCHHHHHHH-HccCCCCcccc
Confidence 45666777764 3334457999999997665543 23334443333
No 41
>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=26.19 E-value=16 Score=22.22 Aligned_cols=25 Identities=20% Similarity=0.356 Sum_probs=19.1
Q ss_pred hhhhHhhhhhcccceeEEEecCCCc
Q 040972 29 FKKAEELSVLCDAEVGVIIFSATGK 53 (87)
Q Consensus 29 ~KKa~ELs~LC~~~v~liv~~~~g~ 53 (87)
+-++.|+.+-||.|+.|+.+-|.|.
T Consensus 39 ~q~v~~i~~DCD~D~ll~~V~~~G~ 63 (75)
T PF01502_consen 39 TQKVVEIRLDCDGDALLFKVEQVGP 63 (75)
T ss_dssp -EEEEEEEE-TTSSEEEEEEEESS-
T ss_pred EEEEEEEEecCCCCeEEEEEEeCCC
Confidence 4556789999999999999988776
No 42
>KOG2292 consensus Oligosaccharyltransferase, STT3 subunit [Posttranslational modification, protein turnover, chaperones]
Probab=26.18 E-value=75 Score=26.59 Aligned_cols=32 Identities=28% Similarity=0.259 Sum_probs=24.5
Q ss_pred hhhhHhhhhhcccceeEEEecCCCceeecCCccHH
Q 040972 29 FKKAEELSVLCDAEVGVIIFSATGKLFESSSSSFI 63 (87)
Q Consensus 29 ~KKa~ELs~LC~~~v~liv~~~~g~~~~~~s~~~~ 63 (87)
-+||+|+...-|||-.||||+. +.-|++++++
T Consensus 584 EekayeImr~lDVdYVLVIFGG---~iGYssDDIN 615 (751)
T KOG2292|consen 584 EEKAYEIMRELDVDYVLVIFGG---LIGYSSDDIN 615 (751)
T ss_pred HHHHHHHHHHcCCCEEEEEecc---cccCCcchhh
Confidence 3789999999999999999974 3445555544
No 43
>cd00106 KISc Kinesin motor domain. 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), in some its is found in the middle (M-type), or C-terminal (C-type). N-type and M-type kinesins are (+) end-directed motors, while C-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 the coil
Probab=25.97 E-value=63 Score=23.60 Aligned_cols=24 Identities=29% Similarity=0.354 Sum_probs=18.3
Q ss_pred hhhcccceeEEEecCC--Cceee-cCC
Q 040972 36 SVLCDAEVGVIIFSAT--GKLFE-SSS 59 (87)
Q Consensus 36 s~LC~~~v~liv~~~~--g~~~~-~~s 59 (87)
+++.|.+++++.|++. ||.|+ +++
T Consensus 73 ~~~~G~~~~i~~yG~tgSGKT~tl~G~ 99 (328)
T cd00106 73 SVLEGYNGTIFAYGQTGSGKTYTMFGS 99 (328)
T ss_pred HHhCCCceeEEEecCCCCCCeEEecCC
Confidence 3467999999999984 67776 554
No 44
>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=25.54 E-value=34 Score=18.80 Aligned_cols=22 Identities=18% Similarity=0.602 Sum_probs=16.3
Q ss_pred hhhhhHhhhhhcccceeEEEec
Q 040972 28 LFKKAEELSVLCDAEVGVIIFS 49 (87)
Q Consensus 28 L~KKa~ELs~LC~~~v~liv~~ 49 (87)
|.+.+..-+=||+++..|.+|.
T Consensus 2 L~~Rs~~kCELC~a~~~L~vy~ 23 (47)
T smart00782 2 LLARCESKCELCGSDSPLVVYA 23 (47)
T ss_pred hhHHcCCcccCcCCCCCceEEe
Confidence 3445556688999999888873
No 45
>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=25.32 E-value=1e+02 Score=19.67 Aligned_cols=28 Identities=25% Similarity=0.461 Sum_probs=19.3
Q ss_pred hhhhHhhhhhc------ccceeEEEecCCCceee
Q 040972 29 FKKAEELSVLC------DAEVGVIIFSATGKLFE 56 (87)
Q Consensus 29 ~KKa~ELs~LC------~~~v~liv~~~~g~~~~ 56 (87)
++.|.|++-.+ +..|+-|++.++|++..
T Consensus 1 m~~al~~A~~~~~~~~~~~pvGaviv~~~g~iv~ 34 (115)
T cd01284 1 MRRALELAEKGRGLTSPNPPVGCVIVDDDGEIVG 34 (115)
T ss_pred CHHHHHHHHhcccccCCCCCEEEEEEeCCCeEEE
Confidence 35677777776 67887777777677543
No 46
>cd03063 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH beta subunit contains a NADH:ubiquinone oxidoreductase (Nuo) F domain C-terminal to a Fd-like domain without the active site cysteines. The absence of conserved metal-binding residues in the putative active site suggests that members of this subfamily have lost the ability to bind iron-sulfur clusters in the N-terminal Fd-like domain. The C-terminal NuoF domain is a component of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. NuoF contains one [4Fe-4S] c
Probab=24.60 E-value=1.6e+02 Score=18.24 Aligned_cols=36 Identities=11% Similarity=0.016 Sum_probs=24.7
Q ss_pred hcccceeEEEecCCCc-eeecCC-ccHHHHHHHHhcCc
Q 040972 38 LCDAEVGVIIFSATGK-LFESSS-SSFITLWFHKSSHI 73 (87)
Q Consensus 38 LC~~~v~liv~~~~g~-~~~~~s-~~~~~vl~~y~~~~ 73 (87)
+|..+-.+.|+.|+|. +|..-. .++.+|++.+...+
T Consensus 44 ~C~~ePlV~V~~p~g~v~Y~~V~~edv~~Iv~~~~~~~ 81 (92)
T cd03063 44 MYWLEPLVEVETPGGRVAYGPVTPADVASLLDAGALEG 81 (92)
T ss_pred ecCCCCEEEEEeCCCcEEEEeCCHHHHHHHHHHHhhcC
Confidence 4777777778777774 444333 68999998876543
No 47
>cd01668 TGS_RelA_SpoT TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after the Threonyl-tRNA Synthetase, GTPase, and SpoT proteins where it occurs. The function of the TGS domain is unknown.
Probab=24.41 E-value=1.2e+02 Score=15.90 Aligned_cols=24 Identities=13% Similarity=0.445 Sum_probs=17.9
Q ss_pred EEecCCCceeecCC-ccHHHHHHHH
Q 040972 46 IIFSATGKLFESSS-SSFITLWFHK 69 (87)
Q Consensus 46 iv~~~~g~~~~~~s-~~~~~vl~~y 69 (87)
.||-|+|..+.++. ..+.+++...
T Consensus 2 ~~~~~~g~~~~~~~~~t~~~~~~~~ 26 (60)
T cd01668 2 YVFTPKGEIIELPAGATVLDFAYAI 26 (60)
T ss_pred EEECCCCCEEEcCCCCCHHHHHHHH
Confidence 57888899888886 5677777644
No 48
>PF02092 tRNA_synt_2f: Glycyl-tRNA synthetase beta subunit; InterPro: IPR015944 The aminoacyl-tRNA synthetases (6.1.1 from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold and are mostly monomeric, while class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet formation, flanked by alpha-helices [], and are mostly dimeric or multimeric. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic aci, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. The 10 class I synthetases are considered to have in common the catalytic domain structure based on the Rossmann fold, which is totally different from the class II catalytic domain structure. The class I synthetases are further divided into three subclasses, a, b and c, according to sequence homology. No conserved structural features for tRNA recognition by class I synthetases have been established. Class-II tRNA synthetases do not share a high degree of similarity, however at least three conserved regions are present [, , ]. In most eubacteria, glycyl-tRNA synthetase (6.1.1.14 from EC) is an alpha2/beta2 tetramer composed of 2 different subunits [, , ] while in archaea, eukaryota and some eubacteria, glycyl-tRNA synthetase is an alpha2 dimer (see IPR002315 from INTERPRO). This entry represents the beta subunit of the tetrameric enzyme. What is most interesting is the lack of similarity between the two types: divergence at the sequence level is so great that it is impossible to infer descent from common genes. The alpha (see IPR002310 from INTERPRO) and beta subunits also lack significant sequence similarity. However, they are translated from a single mRNA [], and a single chain glycyl-tRNA synthetase from Chlamydia trachomatis has been found to have significant similarity with both domains, suggesting divergence from a single polypeptide chain []. This entry represents the beta subunit of glycyl-tRNA synthetase.; GO: 0000166 nucleotide binding, 0004820 glycine-tRNA ligase activity, 0005524 ATP binding, 0006426 glycyl-tRNA aminoacylation, 0005737 cytoplasm
Probab=24.27 E-value=17 Score=29.52 Aligned_cols=66 Identities=15% Similarity=0.067 Sum_probs=51.3
Q ss_pred cccccccchhhhhhHhhhhhcccceeEEEecCC-----CceeecCCccHHHHHHHHhcCcCcchhhhhhhhhcC
Q 040972 19 VTFSKRRRGLFKKAEELSVLCDAEVGVIIFSAT-----GKLFESSSSSFITLWFHKSSHITSFLESKMKVKKAY 87 (87)
Q Consensus 19 ~tf~KRk~gL~KKa~ELs~LC~~~v~liv~~~~-----g~~~~~~s~~~~~vl~~y~~~~~~~~~kkm~~~~~~ 87 (87)
+-+.+|+.-+.+.+.+++--.|..+. .+++ -.+.+||.+-+.++=++|..+|..-....|+.||-|
T Consensus 211 vd~~~Rk~~I~~~i~~~a~~~~~~~~---~d~~LLdEVt~LvE~P~~l~G~Fd~~fL~lP~evlit~M~~hQky 281 (548)
T PF02092_consen 211 VDPEERKEIIREQINKLAKELGGKVI---IDEDLLDEVTNLVEWPVALLGSFDEKFLELPKEVLITSMKEHQKY 281 (548)
T ss_pred CCHHHHHHHHHHHHHHHHHHcCCEec---CCHHHHHHHHHhccCCeEEEEecCHHhhhCCHHHHHHHHHhcceE
Confidence 45788999999999999887765442 2221 136789988778888899999999999999998865
No 49
>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways. Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process
Probab=24.14 E-value=68 Score=21.53 Aligned_cols=24 Identities=21% Similarity=0.108 Sum_probs=17.9
Q ss_pred hhhhcccceeEEEecCCCceeecC
Q 040972 35 LSVLCDAEVGVIIFSATGKLFESS 58 (87)
Q Consensus 35 Ls~LC~~~v~liv~~~~g~~~~~~ 58 (87)
+++.++|++.+++.+.+...-.||
T Consensus 58 i~ta~dad~V~ll~dat~~~~~~p 81 (143)
T PF10662_consen 58 IVTAQDADVVLLLQDATEPRSVFP 81 (143)
T ss_pred HHHHhhCCEEEEEecCCCCCccCC
Confidence 678899999999988766533343
No 50
>PF06020 Roughex: Drosophila roughex protein; InterPro: IPR009259 This family consists of several roughex (RUX) proteins specific to Drosophila species. Roughex can influence the intracellular distribution of cyclin A and is therefore defined as a distinct and specialised cell cycle inhibitor for cyclin A-dependent kinase activity []. Rux is though to regulate the metaphase to anaphase transition during development [].
Probab=23.98 E-value=36 Score=26.00 Aligned_cols=16 Identities=6% Similarity=0.235 Sum_probs=13.1
Q ss_pred hhhcccceeEEEecCC
Q 040972 36 SVLCDAEVGVIIFSAT 51 (87)
Q Consensus 36 s~LC~~~v~liv~~~~ 51 (87)
.-+||.+|||+||...
T Consensus 183 ~~~~~~EICLavYek~ 198 (334)
T PF06020_consen 183 GQVSGFEICLAVYEKG 198 (334)
T ss_pred CccccceEEeeehhhh
Confidence 4579999999999753
No 51
>cd01371 KISc_KIF3 Kinesin motor domain, kinesins II or KIF3_like proteins. Subgroup of kinesins, which form heterotrimers composed of 2 kinesins and one non-motor accessory subunit. Kinesins II play important roles in ciliary transport, and have been implicated in neuronal transport, melanosome transport, the secretory pathway, and 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 this group 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
Probab=23.15 E-value=83 Score=23.35 Aligned_cols=24 Identities=29% Similarity=0.378 Sum_probs=18.9
Q ss_pred hhhcccceeEEEecCC--Cceee-cCC
Q 040972 36 SVLCDAEVGVIIFSAT--GKLFE-SSS 59 (87)
Q Consensus 36 s~LC~~~v~liv~~~~--g~~~~-~~s 59 (87)
+++-|.+++++.|++. ||.|+ +++
T Consensus 76 ~~~~G~n~~i~ayG~tgSGKTyTm~G~ 102 (333)
T cd01371 76 SVLEGYNGTIFAYGQTGTGKTFTMEGV 102 (333)
T ss_pred HHhCCCceeEEecCCCCCCCcEeecCC
Confidence 6788999999999884 67776 443
No 52
>PF13252 DUF4043: Protein of unknown function (DUF4043)
Probab=23.07 E-value=33 Score=26.19 Aligned_cols=29 Identities=28% Similarity=0.220 Sum_probs=21.1
Q ss_pred hhHhhhhhcccceeEEEecC--CCceeecCC
Q 040972 31 KAEELSVLCDAEVGVIIFSA--TGKLFESSS 59 (87)
Q Consensus 31 Ka~ELs~LC~~~v~liv~~~--~g~~~~~~s 59 (87)
.+-.-++|||++++++.|+. +|..|.|..
T Consensus 270 ~~v~ralLlGaQA~~~A~G~~~~~~~~~w~E 300 (341)
T PF13252_consen 270 VAVARALLLGAQALVIAFGKSGSGMRFFWVE 300 (341)
T ss_pred cceeeeeeechhheeeeeeccCCCcccccch
Confidence 44557899999999999987 344555553
No 53
>TIGR03726 strep_RK_lipo putative cross-wall-targeting lipoprotein signal. The YSIRK signal domain targets proteins to the cross-wall, or septum, of dividing Gram-positive bacterial. Lipoprotein signal motifs direct a characteristic N-terminal cleavage and lipid modification for membrane anchoring. This Streptococcal-only signal peptide variant appears to be a hybrid between the two, likely directing protein targeting of nascent surface lipoproteins to the cross-wall. Nearly all members of this family have the characteristic LPXTG cell wall anchor signal at the C-terminus.
Probab=23.04 E-value=31 Score=17.95 Aligned_cols=16 Identities=38% Similarity=0.887 Sum_probs=12.2
Q ss_pred hhhhHhhhhhccccee
Q 040972 29 FKKAEELSVLCDAEVG 44 (87)
Q Consensus 29 ~KKa~ELs~LC~~~v~ 44 (87)
|+|-.-.-+|||+-..
T Consensus 3 FRKsK~~~tLCGa~Lg 18 (34)
T TIGR03726 3 FRKSKKYRTLCGAALG 18 (34)
T ss_pred chhhHHHHHHHHHHHH
Confidence 4777788899998654
No 54
>COG5068 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]
Probab=22.99 E-value=49 Score=26.17 Aligned_cols=46 Identities=24% Similarity=0.265 Sum_probs=37.3
Q ss_pred eEEecCCCccccccccccchhhhhhHhhhhhcccceeEEEecCCCceeecCC
Q 040972 8 IRKIDNITARQVTFSKRRRGLFKKAEELSVLCDAEVGVIIFSATGKLFESSS 59 (87)
Q Consensus 8 ik~I~~~~~R~~tf~KRk~gL~KKa~ELs~LC~~~v~liv~~~~g~~~~~~s 59 (87)
|+.+-|...-..+|+++..| |++.+|+..+-..++....-...|+.
T Consensus 18 i~~~~d~~~ps~~~~~~~~~------~~~~~~~g~~~~~~~~~~~~~~~~~~ 63 (412)
T COG5068 18 IQGDSDANIPSNTINRLSPG------ELSQQNDGKFDVMIFDSKHSVRVYSN 63 (412)
T ss_pred cccccccCCccccccccCcc------cchhhccCCcccccccccccccccCC
Confidence 77788888889999999999 99999999888777765544555554
No 55
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=22.89 E-value=1.5e+02 Score=16.44 Aligned_cols=24 Identities=13% Similarity=0.350 Sum_probs=16.6
Q ss_pred EEEecCCCceeecCC-ccHHHHHHH
Q 040972 45 VIIFSATGKLFESSS-SSFITLWFH 68 (87)
Q Consensus 45 liv~~~~g~~~~~~s-~~~~~vl~~ 68 (87)
+.||-|+|....++. ..+.++...
T Consensus 1 I~v~lpdG~~~~~~~g~T~~d~A~~ 25 (60)
T PF02824_consen 1 IRVYLPDGSIKELPEGSTVLDVAYS 25 (60)
T ss_dssp EEEEETTSCEEEEETTBBHHHHHHH
T ss_pred CEEECCCCCeeeCCCCCCHHHHHHH
Confidence 346679999988776 556666543
No 56
>PF15119 APOC4: Apolipoprotein C4
Probab=22.65 E-value=43 Score=21.18 Aligned_cols=19 Identities=26% Similarity=0.618 Sum_probs=14.8
Q ss_pred ccccchhhhhhHhhh--hhcc
Q 040972 22 SKRRRGLFKKAEELS--VLCD 40 (87)
Q Consensus 22 ~KRk~gL~KKa~ELs--~LC~ 40 (87)
..-|..|++||+.|| +||+
T Consensus 76 ~sSkd~llnk~~sLCPrllC~ 96 (99)
T PF15119_consen 76 RSSKDSLLNKTHSLCPRLLCG 96 (99)
T ss_pred HHhHHHHHHHHHhhCchhhcc
Confidence 456789999999987 5665
No 57
>cd01368 KISc_KIF23_like Kinesin motor domain, KIF23-like subgroup. Members of this group may play a role 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 the coiled-coil domain close to a second tubulin dimer, a
Probab=22.47 E-value=80 Score=23.67 Aligned_cols=25 Identities=20% Similarity=0.344 Sum_probs=19.3
Q ss_pred hhhcccceeEEEecCC--Cceee-cCCc
Q 040972 36 SVLCDAEVGVIIFSAT--GKLFE-SSSS 60 (87)
Q Consensus 36 s~LC~~~v~liv~~~~--g~~~~-~~s~ 60 (87)
.++-|..++++.|+++ ||.|+ ++.+
T Consensus 83 ~~l~G~n~ti~aYGqtGSGKTyTm~G~~ 110 (345)
T cd01368 83 DLLKGKNSLLFTYGVTNSGKTYTMQGSP 110 (345)
T ss_pred HHhCCCceEEEEeCCCCCCCeEEecCCC
Confidence 4678999999999885 67776 4443
No 58
>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=22.41 E-value=89 Score=18.54 Aligned_cols=18 Identities=22% Similarity=0.361 Sum_probs=14.3
Q ss_pred cccceeEEEecCCCceee
Q 040972 39 CDAEVGVIIFSATGKLFE 56 (87)
Q Consensus 39 C~~~v~liv~~~~g~~~~ 56 (87)
-|+++|.|.|++....|+
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 689999999998765543
No 59
>cd02980 TRX_Fd_family Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are soluble low-potential electron carriers containing a single [2Fe-2S] cluster. The exact role of TRX-like Fd is still unclear. It has been suggested that it may be involved in nitrogen fixation. Its homologous domains in large redox enzymes (such as Nuo and hydrogenases) function as electron carriers.
Probab=22.38 E-value=1.2e+02 Score=16.95 Aligned_cols=29 Identities=10% Similarity=0.275 Sum_probs=15.9
Q ss_pred cccceeEEEecCCCceeecCC-ccHHHHHHH
Q 040972 39 CDAEVGVIIFSATGKLFESSS-SSFITLWFH 68 (87)
Q Consensus 39 C~~~v~liv~~~~g~~~~~~s-~~~~~vl~~ 68 (87)
|+.--.++|+ |.+.+|..-+ ..+.+|++.
T Consensus 47 C~~~P~v~i~-~~~~~y~~v~~~~~~~il~~ 76 (77)
T cd02980 47 CGLAPVVVVY-PDGVWYGRVTPEDVEEIVEE 76 (77)
T ss_pred ccCCCEEEEe-CCCeEEccCCHHHHHHHHHh
Confidence 4333333444 5666665444 567777765
No 60
>PF06574 FAD_syn: FAD synthetase; InterPro: IPR015864 Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme [], the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family []. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases []. This entry represents prokaryotic-type FAD synthetase, which occurs primarily as part of a bifunctional enzyme.; GO: 0003919 FMN adenylyltransferase activity, 0009231 riboflavin biosynthetic process; PDB: 2X0K_B 3OP1_B 1T6Z_A 2I1L_A 1T6Y_B 1T6X_B 1S4M_A 1MRZ_A.
Probab=22.32 E-value=97 Score=20.73 Aligned_cols=26 Identities=27% Similarity=0.276 Sum_probs=21.5
Q ss_pred chhhhhhHhhhhhcccceeEEEecCC
Q 040972 26 RGLFKKAEELSVLCDAEVGVIIFSAT 51 (87)
Q Consensus 26 ~gL~KKa~ELs~LC~~~v~liv~~~~ 51 (87)
.-|+++|.+++---+...+|+.|+|.
T Consensus 22 q~Li~~~~~~a~~~~~~~~v~tF~~~ 47 (157)
T PF06574_consen 22 QKLIKKAVEIAKEKGLKSVVLTFDPH 47 (157)
T ss_dssp HHHHHHHHHHHHHCT-EEEEEEESS-
T ss_pred HHHHHHHhhhhhhcccceEEEEcccC
Confidence 45899999999999999999999875
No 61
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=22.07 E-value=1e+02 Score=18.31 Aligned_cols=37 Identities=22% Similarity=0.145 Sum_probs=24.4
Q ss_pred hHhhhhhcccceeEEEecCCCcee-ecCCccHHHHHHHHh
Q 040972 32 AEELSVLCDAEVGVIIFSATGKLF-ESSSSSFITLWFHKS 70 (87)
Q Consensus 32 a~ELs~LC~~~v~liv~~~~g~~~-~~~s~~~~~vl~~y~ 70 (87)
+..|.-+.|++|+.. +++|++. +..+++..++++.+.
T Consensus 21 ~~~l~~~~gvEVh~~--~~~GKiVVtiE~~~~~~~~~~~~ 58 (79)
T PF03927_consen 21 AEALAAIPGVEVHAV--DEDGKIVVTIEAESSEEEVDLID 58 (79)
T ss_dssp HHHHCCSTTEEEEEE--ETTTEEEEEEEESSHHHHHHHHH
T ss_pred HHHHHcCCCcEEEee--CCCCeEEEEEEeCChHHHHHHHH
Confidence 356888899998755 6668864 455555555555544
No 62
>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=21.82 E-value=93 Score=22.93 Aligned_cols=21 Identities=24% Similarity=0.422 Sum_probs=17.3
Q ss_pred hhhcccceeEEEecCC--Cceee
Q 040972 36 SVLCDAEVGVIIFSAT--GKLFE 56 (87)
Q Consensus 36 s~LC~~~v~liv~~~~--g~~~~ 56 (87)
+++-|.+++++.|+++ ||.|+
T Consensus 75 ~~~~G~n~~i~ayG~tgSGKTyT 97 (319)
T cd01376 75 HLLSGQNATVFAYGSTGAGKTHT 97 (319)
T ss_pred HHhCCCceEEEEECCCCCCCcEE
Confidence 5677999999999884 67776
No 63
>smart00129 KISc Kinesin motor, catalytic domain. ATPase. Microtubule-dependent molecular motors that play important roles in intracellular transport of organelles and in cell division.
Probab=21.67 E-value=85 Score=23.06 Aligned_cols=23 Identities=26% Similarity=0.449 Sum_probs=17.7
Q ss_pred hhcccceeEEEecCC--Cceee-cCC
Q 040972 37 VLCDAEVGVIIFSAT--GKLFE-SSS 59 (87)
Q Consensus 37 ~LC~~~v~liv~~~~--g~~~~-~~s 59 (87)
++-|.++++++|++. ||.|+ +++
T Consensus 75 ~~~G~~~~i~~yG~tgSGKT~tl~G~ 100 (335)
T smart00129 75 VLEGYNATIFAYGQTGSGKTYTMSGT 100 (335)
T ss_pred HhcCCceeEEEeCCCCCCCceEecCC
Confidence 578999999999984 67665 443
No 64
>COG1918 FeoA Fe2+ transport system protein A [Inorganic ion transport and metabolism]
Probab=21.64 E-value=1.3e+02 Score=18.00 Aligned_cols=31 Identities=16% Similarity=0.248 Sum_probs=27.3
Q ss_pred chhhhhhHhhhhhcccceeEEEecCCCceee
Q 040972 26 RGLFKKAEELSVLCDAEVGVIIFSATGKLFE 56 (87)
Q Consensus 26 ~gL~KKa~ELs~LC~~~v~liv~~~~g~~~~ 56 (87)
.++.++-.++-+.-|+++.++--.|-|++..
T Consensus 21 ~~~~~RL~~mG~~~G~~i~vi~~aplgdPi~ 51 (75)
T COG1918 21 NGLRRRLLSMGIVPGASITVVRKAPLGDPIL 51 (75)
T ss_pred HHHHHHHHHcCCCCCCEEEEEEecCCCCCEE
Confidence 4899999999999999999999999886543
No 65
>COG1438 ArgR Arginine repressor [Transcription]
Probab=21.49 E-value=53 Score=22.41 Aligned_cols=18 Identities=17% Similarity=0.290 Sum_probs=15.0
Q ss_pred HhhhhhcccceeEEEecC
Q 040972 33 EELSVLCDAEVGVIIFSA 50 (87)
Q Consensus 33 ~ELs~LC~~~v~liv~~~ 50 (87)
.=|.++||.|.++|+.-.
T Consensus 118 eIlGTIaGdDTilVi~r~ 135 (150)
T COG1438 118 EILGTIAGDDTILVICRS 135 (150)
T ss_pred hhheeeeCCCeEEEEecC
Confidence 458999999999998754
No 66
>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=21.45 E-value=59 Score=15.96 Aligned_cols=18 Identities=28% Similarity=0.318 Sum_probs=12.2
Q ss_pred ceeEEEecCCCceeecCC
Q 040972 42 EVGVIIFSATGKLFESSS 59 (87)
Q Consensus 42 ~v~liv~~~~g~~~~~~s 59 (87)
.-.-..+||+|+-..|.+
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 344577899999877765
No 67
>PF00360 PHY: Phytochrome region; InterPro: IPR013515 Phytochrome belongs to a family of plant photoreceptors that mediate physiological and developmental responses to changes in red and far-red light conditions []. The protein undergoes reversible photochemical conversion between a biologically-inactive red light-absorbing form and the active far-red light-absorbing form. Phytochrome is a dimer of identical 124 kDa subunits, each of which contains a linear tetrapyrrole chromophore, covalently-attached via a Cys residue. This domain represents a region specific to phytochrome proteins.; GO: 0008020 G-protein coupled photoreceptor activity, 0006355 regulation of transcription, DNA-dependent, 0009584 detection of visible light, 0018298 protein-chromophore linkage; PDB: 3C2W_G 3NHQ_B 3G6O_B 3IBR_A 2VEA_A 3ZQ5_A.
Probab=21.30 E-value=85 Score=21.47 Aligned_cols=38 Identities=18% Similarity=0.310 Sum_probs=25.7
Q ss_pred chhhhhhHhhhhhcccceeEEEecCCCceeecCC-ccHHHH
Q 040972 26 RGLFKKAEELSVLCDAEVGVIIFSATGKLFESSS-SSFITL 65 (87)
Q Consensus 26 ~gL~KKa~ELs~LC~~~v~liv~~~~g~~~~~~s-~~~~~v 65 (87)
.+|..-+..|.-|.+|+=++|+++ |+++.++. |+...|
T Consensus 20 ~~l~~~~~~ll~l~~AdG~al~~~--g~~~~~G~~P~~~~i 58 (182)
T PF00360_consen 20 EALISQAPDLLDLVDADGVALVID--GEVYTFGETPPEEQI 58 (182)
T ss_dssp HHHCTTCCCHHHCTT-SEEEEEET--TEEEEEESS--HHHH
T ss_pred HhhHhccHHHHhhccCCEEEEEEC--CEEEEecCCcCHHHH
Confidence 455666778889999999888887 67777776 544433
No 68
>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=20.86 E-value=86 Score=25.02 Aligned_cols=33 Identities=12% Similarity=0.224 Sum_probs=22.1
Q ss_pred hhhhcccceeE---------EEecCCCceeecCCccHHHHHH
Q 040972 35 LSVLCDAEVGV---------IIFSATGKLFESSSSSFITLWF 67 (87)
Q Consensus 35 Ls~LC~~~v~l---------iv~~~~g~~~~~~s~~~~~vl~ 67 (87)
||-.|++.++- .+.-=+|+.|.|+|+.-+.+-+
T Consensus 382 ~c~vC~~p~~~~~~~~~~~~~~~ey~G~~y~FCS~~C~~~F~ 423 (465)
T cd01057 382 LCNVCQVPCVFTEDLTAEAPRVLEYNGRKYHFCSEGCEWIFE 423 (465)
T ss_pred CCCCCCCeeccccCcccccceEEEECCEEEEecCHHHHHHHH
Confidence 67778887762 2222269999999976555543
No 69
>cd00173 SH2 Src homology 2 domains; Signal transduction, involved in recognition of phosphorylated tyrosine (pTyr). SH2 domains typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.
Probab=20.30 E-value=1.3e+02 Score=17.28 Aligned_cols=43 Identities=21% Similarity=0.091 Sum_probs=25.0
Q ss_pred hHhhhhhccccee-EEE-ecCCCceeec-CC--ccHHHHHHHHhcCcC
Q 040972 32 AEELSVLCDAEVG-VII-FSATGKLFES-SS--SSFITLWFHKSSHIT 74 (87)
Q Consensus 32 a~ELs~LC~~~v~-liv-~~~~g~~~~~-~s--~~~~~vl~~y~~~~~ 74 (87)
..-||+.++-.+. ..| ..++|..+.. .. +++.++|+.|...+.
T Consensus 35 ~~~Lsv~~~~~v~H~~I~~~~~~~~~~~~~~~f~sl~eLv~~y~~~~~ 82 (94)
T cd00173 35 DYVLSVRVKGKVKHYRIERTDDGYYLLGEGRSFPSLPELIEHYQKNPL 82 (94)
T ss_pred CEEEEEEECCEEEEEEEEECCCCeEEecCCCccCCHHHHHHHHhhCcc
Confidence 3456666665552 233 3333333322 22 899999999998773
No 70
>cd01372 KISc_KIF4 Kinesin motor domain, KIF4-like subfamily. Members of this group seem to perform a variety of functions, and have been implicated in neuronal organelle transport and chromosome segregation during mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain,
Probab=20.20 E-value=1.6e+02 Score=21.72 Aligned_cols=22 Identities=18% Similarity=0.370 Sum_probs=17.9
Q ss_pred hhhcccceeEEEecCC--Cceeec
Q 040972 36 SVLCDAEVGVIIFSAT--GKLFES 57 (87)
Q Consensus 36 s~LC~~~v~liv~~~~--g~~~~~ 57 (87)
+++-|.+++++.|++. ||.|+.
T Consensus 68 ~~~~G~n~~i~ayG~tgSGKT~Tm 91 (341)
T cd01372 68 GLFEGYNATVLAYGQTGSGKTYTM 91 (341)
T ss_pred HHhCCCccceeeecCCCCCCcEEe
Confidence 5688999999999884 677774
Done!