Query psy15415
Match_columns 128
No_of_seqs 159 out of 707
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 20:26:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15415.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15415hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00059 FH Forkhead (FH), also 100.0 2.8E-31 6E-36 181.5 3.7 56 2-57 21-78 (78)
2 PF00250 Fork_head: Fork head 100.0 3.5E-30 7.6E-35 181.7 3.0 67 2-69 21-89 (96)
3 smart00339 FH FORKHEAD. FORKHE 100.0 2.4E-29 5.2E-34 175.4 3.7 59 2-60 21-81 (89)
4 KOG3563|consensus 99.9 2.4E-28 5.3E-33 205.7 1.7 76 2-79 193-270 (454)
5 KOG2294|consensus 99.9 6.8E-27 1.5E-31 196.4 2.0 66 1-67 149-218 (454)
6 KOG3562|consensus 99.9 2E-26 4.3E-31 184.4 3.0 67 2-70 33-101 (277)
7 COG5025 Transcription factor o 99.7 5.6E-18 1.2E-22 150.8 1.4 66 2-67 357-424 (610)
8 KOG4385|consensus 99.6 1.1E-17 2.3E-22 145.4 -1.2 55 2-59 388-442 (581)
9 COG5025 Transcription factor o 99.1 1.2E-11 2.6E-16 110.6 -0.3 65 2-67 106-172 (610)
10 smart00258 SAND SAND domain. 48.2 6.4 0.00014 26.7 0.2 16 21-36 47-62 (73)
11 PF01342 SAND: SAND domain; I 42.1 10 0.00023 25.8 0.5 13 21-33 56-68 (82)
12 PF05066 HARE-HTH: HB1, ASXL, 40.2 21 0.00045 22.9 1.7 40 3-43 18-62 (72)
13 PF06531 DUF1108: Protein of u 29.1 38 0.00081 23.8 1.5 13 4-16 61-73 (86)
14 cd01770 p47_UBX p47-like ubiqu 28.5 42 0.00091 22.4 1.7 15 3-17 25-39 (79)
15 PF10523 BEN: BEN domain; Int 27.7 51 0.0011 21.0 2.0 25 4-32 42-66 (79)
16 PF10826 DUF2551: Protein of u 25.1 51 0.0011 23.0 1.6 17 2-18 25-41 (83)
17 cd01767 UBX UBX (ubiquitin reg 24.8 53 0.0011 21.2 1.6 13 4-16 24-36 (77)
18 PF00538 Linker_histone: linke 24.2 52 0.0011 21.5 1.5 16 3-18 22-37 (77)
19 PF12990 DUF3874: Domain of un 23.9 56 0.0012 22.0 1.6 17 2-18 25-41 (73)
No 1
>cd00059 FH Forkhead (FH), also known as a "winged helix". FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix.
Probab=99.97 E-value=2.8e-31 Score=181.46 Aligned_cols=56 Identities=36% Similarity=0.688 Sum_probs=54.2
Q ss_pred cccHHHHHHHHHhcCCCccCCCcchhhhhhhhcccCccccccccc--CCCCcceEeeC
Q psy15415 2 ALTANLRLFFHRERFPYYNQNDDRWKNSVRHNLSINPHFRKGVKA--SQGAGHLWNLS 57 (128)
Q Consensus 2 rLTL~eIY~~I~~~fPyyr~~~~gWkNSIRHNLSln~~F~Kv~r~--~~Gkg~~W~i~ 57 (128)
+|||+|||+||+++||||+.+++|||||||||||+|+||+||+++ ++|||+||+||
T Consensus 21 ~lTL~eIy~~I~~~~pyyr~~~~gWknSIRHnLS~n~~F~kv~r~~~~~gkg~~W~i~ 78 (78)
T cd00059 21 RLTLSEIYKWISDNFPYFRDAPAGWQNSIRHNLSLNKCFVKVPREPDEPGKGSYWTLD 78 (78)
T ss_pred CeeHHHHHHHHHHhCCccccCCCCCccceeEecccccceEECCCCCCCCCCCCeeeeC
Confidence 699999999999999999999999999999999999999999997 68999999997
No 2
>PF00250 Fork_head: Fork head domain; InterPro: IPR001766 The fork head protein of Drosophila melanogaster, a transcription factor that promotes terminal rather than segmental development, contains neither homeodomains nor zinc-fingers characteristic of other transcription factors []. Instead, it contains a distinct type of DNA-binding region, containing around 100 amino acids, which has since been identified in a number of transcription factors (including D. melanogaster FD1-5, mammalian HNF-3, human HTLF, Saccharomyces cerevisiae HCM1, etc.). This is referred to as the fork head domain but is also known as a 'winged helix' [, , ]. The fork head domain binds B-DNA as a monomer [], but shows no similarity to previously identified DNA-binding motifs. Although the domain is found in several different transcription factors, a common function is their involvement in early developmental decisions of cell fates during embryogenesis [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2UZK_A 2K86_A 1JXS_A 2C6Y_A 2A3S_A 2D2W_A 2KIU_A 1VTN_C 2A07_J 2AS5_F ....
Probab=99.96 E-value=3.5e-30 Score=181.69 Aligned_cols=67 Identities=36% Similarity=0.653 Sum_probs=58.1
Q ss_pred cccHHHHHHHHHhcCCCccCCCcchhhhhhhhcccCcccccccc--cCCCCcceEeeCCCchHHHhhhcc
Q psy15415 2 ALTANLRLFFHRERFPYYNQNDDRWKNSVRHNLSINPHFRKGVK--ASQGAGHLWNLSDMEPVEDASKSN 69 (128)
Q Consensus 2 rLTL~eIY~~I~~~fPyyr~~~~gWkNSIRHNLSln~~F~Kv~r--~~~Gkg~~W~i~~~~~~e~~~~~~ 69 (128)
+|||+|||+||+++||||+.+.+|||||||||||+|+||+||++ +++|||+||+|+++. .+...+..
T Consensus 21 ~Ltl~eIy~~i~~~~pyyr~~~~~WknSIRHnLS~~~~F~kv~~~~~~~gkg~~W~i~~~~-~~~~~~~~ 89 (96)
T PF00250_consen 21 RLTLSEIYEWIEENFPYYRDASKGWKNSIRHNLSLNKCFVKVPRDPSEPGKGSYWTIDPEA-IEEFEKGR 89 (96)
T ss_dssp EBEHHHHHHHHHHHCGHHHCTHCHHHHHHHHHHHHSTTEEEESCCTSSSSSSEEEEE-CTH-HHHHHHSC
T ss_pred CccHHHHHHHHHHhhccccccchhhhhHHhhhccccceeeecCcCCCCCCCceeEEeCHHH-HHHHhcch
Confidence 69999999999999999999999999999999999999999999 458999999999973 44444333
No 3
>smart00339 FH FORKHEAD. FORKHEAD, also known as a "winged helix"
Probab=99.95 E-value=2.4e-29 Score=175.39 Aligned_cols=59 Identities=37% Similarity=0.678 Sum_probs=56.0
Q ss_pred cccHHHHHHHHHhcCCCccCCCcchhhhhhhhcccCccccccccc--CCCCcceEeeCCCc
Q psy15415 2 ALTANLRLFFHRERFPYYNQNDDRWKNSVRHNLSINPHFRKGVKA--SQGAGHLWNLSDME 60 (128)
Q Consensus 2 rLTL~eIY~~I~~~fPyyr~~~~gWkNSIRHNLSln~~F~Kv~r~--~~Gkg~~W~i~~~~ 60 (128)
+|||+|||+||+++||||+.+++|||||||||||+|+||+||++. ++|||+||+|+|+.
T Consensus 21 ~ltl~~Iy~~I~~~~pyy~~~~~~WknSIRHnLS~n~~F~kv~~~~~~~gkg~~W~i~~~~ 81 (89)
T smart00339 21 RLTLSEIYKWIEDNFPYYRENRAGWQNSIRHNLSLNDCFVKVPREGDRPGKGSYWTLDPDA 81 (89)
T ss_pred CeeHHHHHHHHHHhCchhhcCccccccccccccchhhceeecCcCCCCCCCCCEEEECccH
Confidence 799999999999999999999999999999999999999999985 46999999999974
No 4
>KOG3563|consensus
Probab=99.94 E-value=2.4e-28 Score=205.74 Aligned_cols=76 Identities=32% Similarity=0.533 Sum_probs=67.1
Q ss_pred cccHHHHHHHHHhcCCCccCCCcchhhhhhhhcccCccccccccc--CCCCcceEeeCCCchHHHhhhcccccccccccc
Q psy15415 2 ALTANLRLFFHRERFPYYNQNDDRWKNSVRHNLSINPHFRKGVKA--SQGAGHLWNLSDMEPVEDASKSNWVSIKVTGVK 79 (128)
Q Consensus 2 rLTL~eIY~~I~~~fPyyr~~~~gWkNSIRHNLSln~~F~Kv~r~--~~Gkg~~W~i~~~~~~e~~~~~~~~~rk~~~~~ 79 (128)
+|||+|||+||++.|||||.+...|||||||.||+|+||+||+|. -+|||+||++.|+ ...+|...+.-||++++|
T Consensus 193 mLTLSEIYqwIMDLFPyYrqNQQRWQNSIRHSLSFNDCFVKVaRSPDKPGKGSfWTLHpd--sGNMFENGCYLRRQKRFK 270 (454)
T KOG3563|consen 193 MLTLSEIYQWIMDLFPYYRQNQQRWQNSIRHSLSFNDCFVKVARSPDKPGKGSFWTLHPD--SGNMFENGCYLRRQKRFK 270 (454)
T ss_pred ceeHHHHHHHHHHhhhHhhhhHHHHHhhhhhhccccceeeeccCCCCCCCCccceeecCC--cCcccccchhehhhhhhh
Confidence 699999999999999999999999999999999999999999996 4899999999996 467776666666665554
No 5
>KOG2294|consensus
Probab=99.93 E-value=6.8e-27 Score=196.38 Aligned_cols=66 Identities=35% Similarity=0.615 Sum_probs=58.4
Q ss_pred CcccHHHHHHHHHh-cCCCccCCC-cchhhhhhhhcccCcccccccccC--CCCcceEeeCCCchHHHhhh
Q psy15415 1 MALTANLRLFFHRE-RFPYYNQND-DRWKNSVRHNLSINPHFRKGVKAS--QGAGHLWNLSDMEPVEDASK 67 (128)
Q Consensus 1 ~rLTL~eIY~~I~~-~fPyyr~~~-~gWkNSIRHNLSln~~F~Kv~r~~--~Gkg~~W~i~~~~~~e~~~~ 67 (128)
.+|||+|||+||.. +|||||.+. .|||||||||||||+||+||+++. +|||+||+|||+. ...+|.
T Consensus 149 krLtLs~Iy~~i~~~~fpyyr~~~~~gWqNSIRHNLSLn~cF~Kvpr~~~~~gKg~~W~ldP~~-~~~~~~ 218 (454)
T KOG2294|consen 149 KRLTLGGIYFYILLEHFPYYRDANMPGWKNSIRHNLSLNKCFVKVPRERGRPGKGNYWTLDPDD-ENNMFD 218 (454)
T ss_pred cceeecCeeEEEEeccccccccCCCccchhhcccccccccCccccCCcccCCCCCCccccCcch-hccccc
Confidence 38999999999995 999999999 999999999999999999999963 6999999999962 332555
No 6
>KOG3562|consensus
Probab=99.92 E-value=2e-26 Score=184.41 Aligned_cols=67 Identities=36% Similarity=0.592 Sum_probs=61.1
Q ss_pred cccHHHHHHHHHhcCCCccCCCcchhhhhhhhcccCccccccccc--CCCCcceEeeCCCchHHHhhhccc
Q psy15415 2 ALTANLRLFFHRERFPYYNQNDDRWKNSVRHNLSINPHFRKGVKA--SQGAGHLWNLSDMEPVEDASKSNW 70 (128)
Q Consensus 2 rLTL~eIY~~I~~~fPyyr~~~~gWkNSIRHNLSln~~F~Kv~r~--~~Gkg~~W~i~~~~~~e~~~~~~~ 70 (128)
+|.|+|||+||+++|||||.+...||||+|||||+|+||+||||+ .+|||+||++.|. +-++|..+.
T Consensus 33 mLPLseIYkfImDrFPfYRkNTQrWQNSLRHNLSFNDCFIKiPRr~drpGKGsyWalHP~--a~dMFENGS 101 (277)
T KOG3562|consen 33 MLPLSEIYKFIMDRFPFYRKNTQRWQNSLRHNLSFNDCFIKIPRRPDRPGKGSYWALHPS--AFDMFENGS 101 (277)
T ss_pred cCcHHHHHHHHHhhCchhhhchHHHHHHhhccccccceeeecCCCCCCCCCccceeeccc--hhhhcccch
Confidence 588999999999999999999999999999999999999999996 5899999999995 667776544
No 7
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.68 E-value=5.6e-18 Score=150.79 Aligned_cols=66 Identities=32% Similarity=0.585 Sum_probs=61.1
Q ss_pred cccHHHHHHHHHhcCCCccCCCcchhhhhhhhcccCccccccccc--CCCCcceEeeCCCchHHHhhh
Q psy15415 2 ALTANLRLFFHRERFPYYNQNDDRWKNSVRHNLSINPHFRKGVKA--SQGAGHLWNLSDMEPVEDASK 67 (128)
Q Consensus 2 rLTL~eIY~~I~~~fPyyr~~~~gWkNSIRHNLSln~~F~Kv~r~--~~Gkg~~W~i~~~~~~e~~~~ 67 (128)
+|+|.+||.||..+|||||.++.+|+||||||||+|++|.|||++ ++|||+||.|++++..+...+
T Consensus 357 kmsls~Iy~~i~s~~pyYr~~p~~w~nSiRhnlSlNksf~kvP~sa~~pGKg~fw~i~~s~~~~~~sk 424 (610)
T COG5025 357 KMTLSEIYSWISSNLPYYRHKPTAWQNSIRHNLSLNKSFEKVPRSASQPGKGCFWKIDYSYIYEKESK 424 (610)
T ss_pred ccccccccccccccchhhccCCcccCchhhhhhhhccccccCCCCcCCCCCcccCccChhhhhhhccc
Confidence 589999999999999999999999999999999999999999997 589999999999876666554
No 8
>KOG4385|consensus
Probab=99.65 E-value=1.1e-17 Score=145.42 Aligned_cols=55 Identities=33% Similarity=0.623 Sum_probs=52.3
Q ss_pred cccHHHHHHHHHhcCCCccCCCcchhhhhhhhcccCcccccccccCCCCcceEeeCCC
Q psy15415 2 ALTANLRLFFHRERFPYYNQNDDRWKNSVRHNLSINPHFRKGVKASQGAGHLWNLSDM 59 (128)
Q Consensus 2 rLTL~eIY~~I~~~fPyyr~~~~gWkNSIRHNLSln~~F~Kv~r~~~Gkg~~W~i~~~ 59 (128)
+|||+|||.|+++.|.|||.+.+.|||+||||||+++||++|+. -||.-|++|+.
T Consensus 388 QLTLNEIY~WFTrtFAYFRRNaATWKnAVRHNLSLHKCF~RVEn---vkgavwtvDe~ 442 (581)
T KOG4385|consen 388 QLTLNEIYNWFTRTFAYFRRNAATWKNAVRHNLSLHKCFVRVEN---VKGAVWTVDER 442 (581)
T ss_pred hccHHHHHHHHHHHHHHHhccchhHhHHHhhhhHHHHHHHHHHH---Hhcceeeeehh
Confidence 69999999999999999999999999999999999999999877 48999999984
No 9
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.10 E-value=1.2e-11 Score=110.61 Aligned_cols=65 Identities=32% Similarity=0.506 Sum_probs=57.5
Q ss_pred cccHHHHHHHHHhcCCCccCCCcchhhhhhhhcccCccccccccc--CCCCcceEeeCCCchHHHhhh
Q psy15415 2 ALTANLRLFFHRERFPYYNQNDDRWKNSVRHNLSINPHFRKGVKA--SQGAGHLWNLSDMEPVEDASK 67 (128)
Q Consensus 2 rLTL~eIY~~I~~~fPyyr~~~~gWkNSIRHNLSln~~F~Kv~r~--~~Gkg~~W~i~~~~~~e~~~~ 67 (128)
.|||..||.||-..|.||.....+|+|||||||++++.|.||.+. ..++|.||.|.|.. .+.+++
T Consensus 106 ~lt~s~~~~~~~~~~~~~~k~~~~~~~sIr~Nls~~~a~~~i~g~~g~~~~g~~~~igP~~-~~~~l~ 172 (610)
T COG5025 106 PLTLSKIYTWIHNTFFYYAKVVSRWQNSIRHNLSLNDAFIKIEGRNGAKVKGHFWSIGPGH-ETQFLK 172 (610)
T ss_pred CCcccceeeeeeecccccccccchhhhhhhcccccCceEEEEeccCCccccceeeccCCCc-cceeec
Confidence 689999999999999999999999999999999999999999876 35999999999973 333433
No 10
>smart00258 SAND SAND domain.
Probab=48.23 E-value=6.4 Score=26.69 Aligned_cols=16 Identities=31% Similarity=0.486 Sum_probs=12.2
Q ss_pred CCCcchhhhhhhhccc
Q psy15415 21 QNDDRWKNSVRHNLSI 36 (128)
Q Consensus 21 ~~~~gWkNSIRHNLSl 36 (128)
...+.|+-|||+|=+.
T Consensus 47 ~~~K~WK~sIR~~g~~ 62 (73)
T smart00258 47 GKSKDWKRSIRCGGSS 62 (73)
T ss_pred cccCCcchheeECCcc
Confidence 3458999999988543
No 11
>PF01342 SAND: SAND domain; InterPro: IPR000770 The SAND domain (named after Sp100, AIRE-1, NucP41/75, DEAF-1) is a conserved ~80 residue region found in a number of nuclear proteins, many of which function in chromatin-dependent transcriptional control. These include proteins linked to various human diseases, such as the Sp100 (Speckled protein 100 kDa), NUDR (Nuclear DEAF-1 related), GMEB (Glucocorticoid Modulatory Element Binding) proteins and AIRE-1 (Autoimmune regulator 1) proteins. Proteins containing the SAND domain have a modular structure; the SAND domain can be associated with a number of other modules, including the bromodomain, the PHD finger and the MYND finger. Because no SAND domain has been found in yeast, it is thought that the SAND domain could be restricted to animal phyla. Many SAND domain-containing proteins, including NUDR, DEAF-1 (Deformed epidermal autoregulatory factor-1) and GMEB, have been shown to bind DNA sequences specifically. The SAND domain has been proposed to mediate the DNA binding activity of these proteins [, ]. The resolution of the 3D structure of the SAND domain from Sp100b has revealed that it consists of a novel alpha/beta fold. The SAND domain adopts a compact fold consisting of a strongly twisted, five-stranded antiparallel beta-sheet with four alpha-helices packing against one side of the beta-sheet. The opposite side of the beta-sheet is solvent exposed. The beta-sheet and alpha-helical parts of the structure form two distinct regions. Multiple hydrophobic residues pack between these regions to form a structural core. A conserved KDWK sequence motif is found within the alpha-helical, positively charged surface patch. The DNA binding surface has been mapped to the alpha-helical region encompassing the KDWK motif [].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 1OQJ_B 1UFN_A 1H5P_A.
Probab=42.12 E-value=10 Score=25.81 Aligned_cols=13 Identities=31% Similarity=0.703 Sum_probs=9.4
Q ss_pred CCCcchhhhhhhh
Q psy15415 21 QNDDRWKNSVRHN 33 (128)
Q Consensus 21 ~~~~gWkNSIRHN 33 (128)
...+.||.|||++
T Consensus 56 ~~sK~WK~SIr~~ 68 (82)
T PF01342_consen 56 GSSKDWKRSIRCG 68 (82)
T ss_dssp CTCS-HHHHSEET
T ss_pred ccCCCCCccEEEC
Confidence 4557899999973
No 12
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=40.22 E-value=21 Score=22.92 Aligned_cols=40 Identities=18% Similarity=0.093 Sum_probs=25.8
Q ss_pred ccHHHHHHHHHhcCCCccCCCcchhhhhhhhc----c-cCcccccc
Q psy15415 3 LTANLRLFFHRERFPYYNQNDDRWKNSVRHNL----S-INPHFRKG 43 (128)
Q Consensus 3 LTL~eIY~~I~~~fPyyr~~~~gWkNSIRHNL----S-ln~~F~Kv 43 (128)
||.+||++.|.+.--| ....+...++|+-.| . .+..|++|
T Consensus 18 m~~~eI~~~i~~~~~~-~~~~k~p~~~i~a~ly~~~~~~d~~F~~v 62 (72)
T PF05066_consen 18 MTFKEIWEEIQERGLY-KKSGKTPEATIAAQLYTDIKNEDSRFVKV 62 (72)
T ss_dssp EEHHHHHHHHHHHHTS----GGGGGHHHH-HHHHHHH-T-SS-EES
T ss_pred cCHHHHHHHHHHhCCC-CcccCCHHHHHHHHHHHHcccCCCCEEEe
Confidence 7899999999987654 333677778887333 3 45578886
No 13
>PF06531 DUF1108: Protein of unknown function (DUF1108); InterPro: IPR009494 This entry is represented by Bacteriophage 92, Orf49. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial proteins from Staphylococcus aureus as well as a number of phage proteins. The function of this family is unknown.
Probab=29.12 E-value=38 Score=23.76 Aligned_cols=13 Identities=8% Similarity=-0.105 Sum_probs=10.3
Q ss_pred cHHHHHHHHHhcC
Q psy15415 4 TANLRLFFHRERF 16 (128)
Q Consensus 4 TL~eIY~~I~~~f 16 (128)
-.+.||+||+++-
T Consensus 61 i~~aiyewIE~nT 73 (86)
T PF06531_consen 61 INQAIYEWIEENT 73 (86)
T ss_pred HHHHHHHHHHhCc
Confidence 3578999999874
No 14
>cd01770 p47_UBX p47-like ubiquitin domain. p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=28.50 E-value=42 Score=22.37 Aligned_cols=15 Identities=13% Similarity=-0.137 Sum_probs=12.5
Q ss_pred ccHHHHHHHHHhcCC
Q psy15415 3 LTANLRLFFHRERFP 17 (128)
Q Consensus 3 LTL~eIY~~I~~~fP 17 (128)
=||.+||+||....|
T Consensus 25 ~tv~~l~~~v~~~~~ 39 (79)
T cd01770 25 HRVSDVRDFIVNARP 39 (79)
T ss_pred CcHHHHHHHHHHhCC
Confidence 378999999998765
No 15
>PF10523 BEN: BEN domain; InterPro: IPR018379 The BEN domain is found in diverse proteins including: SMAR1 (Scaffold/Matrix attachment region-binding protein 1; also known as BANP), a tumour-suppressor MAR-binding protein that down-regulates Cyclin D1 expression by recruiting HDAC1-mSin3A co-repressor complex at Cyclin D1 promoter locus; SMAR1 is the target of prostaglandin A2 (PGA2) induced growth arrest [, ]. NAC1, a novel member of the POZ/BTB (Pox virus and Zinc finger/Bric-a-bracTramtrack Broad complex), but which varies from other proteins of this class in that it lacks the characteristic DNA-binding motif []. Mod(mdg4) isoform C, the modifier of the mdg4 locus in Drosophila melanogaster (Fruit fly), where mdg4 encodes chromatin proteins which are involved in position effect variegation, establishment of chromatin boundaries, nerve path finding, meiotic chromosome pairing and apoptosis []. Trans-splicing of Mod(mdg4) produces at least 26 transcripts. E5R protein from Chordopoxvirus virosomes, which is found in cytoplasmic sites of viral DNA replication []. Several proteins of polydnaviruses. The BEN domain is predicted to function as an adaptor for the higher-order structuring of chromatin, and recruitment of chromatin modifying factors in transcriptional regulation. It has been suggested to mediate protein-DNA and protein-protein interactions during chromatin organisation and transcription. The presence of BEN domains in a poxviral early virosomal protein and in polydnaviral proteins also suggests a possible role in the organisation of viral DNA during replication or transcription. They are generally linked to other globular domains with functions related to transcriptional regulation and chromatin structure, such as BTB, C4DM, and C2H2 fingers []. This domain is predicted to form an all-alpha fold with four conserved helices. Its conservation pattern revealed several conserved residues, most of which have hydrophobic side-chains and are likely to stabilise the fold through helix-helix packing [].
Probab=27.70 E-value=51 Score=20.97 Aligned_cols=25 Identities=24% Similarity=0.519 Sum_probs=20.5
Q ss_pred cHHHHHHHHHhcCCCccCCCcchhhhhhh
Q psy15415 4 TANLRLFFHRERFPYYNQNDDRWKNSVRH 32 (128)
Q Consensus 4 TL~eIY~~I~~~fPyyr~~~~gWkNSIRH 32 (128)
.|+.|..+|..+||--. ..|+ .|+.
T Consensus 42 kl~~I~~~v~~~~~~~~---~~w~-~~~~ 66 (79)
T PF10523_consen 42 KLSAIRNYVEERFPSEK---RKWR-ECRQ 66 (79)
T ss_pred HHHHHHHHHHHHCCcch---hhHH-HHHH
Confidence 47899999999999876 7888 5554
No 16
>PF10826 DUF2551: Protein of unknown function (DUF2551) ; InterPro: IPR020501 This entry contains proteins with no known function.
Probab=25.12 E-value=51 Score=22.97 Aligned_cols=17 Identities=18% Similarity=0.114 Sum_probs=14.6
Q ss_pred cccHHHHHHHHHhcCCC
Q psy15415 2 ALTANLRLFFHRERFPY 18 (128)
Q Consensus 2 rLTL~eIY~~I~~~fPy 18 (128)
.+|..|||+.+.+.|+-
T Consensus 25 ~~T~~di~e~L~~~f~v 41 (83)
T PF10826_consen 25 KFTTDDIYERLKEKFDV 41 (83)
T ss_pred CeeHHHHHHHHHHHcCc
Confidence 47999999999999653
No 17
>cd01767 UBX UBX (ubiquitin regulatory X) domain. The UBX (ubiquitin regulatory X) domain has a beta-grasp fold that is structurally quite similar to ubiquitin although UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins. Most UBX-containing proteins including p47, FAF1, and SAKS1 (Y33K) also contain a UBA (ubiquitin-associated) domain and are thought to serve as adaptor molecules that shuttle proteins to the proteasome for degradation.
Probab=24.76 E-value=53 Score=21.22 Aligned_cols=13 Identities=8% Similarity=-0.309 Sum_probs=11.1
Q ss_pred cHHHHHHHHHhcC
Q psy15415 4 TANLRLFFHRERF 16 (128)
Q Consensus 4 TL~eIY~~I~~~f 16 (128)
||.+||+||...-
T Consensus 24 tl~~l~~fv~~~~ 36 (77)
T cd01767 24 KLSDVRDFVESNG 36 (77)
T ss_pred CHHHHHHHHHHcC
Confidence 7899999998664
No 18
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=24.24 E-value=52 Score=21.50 Aligned_cols=16 Identities=0% Similarity=0.036 Sum_probs=13.8
Q ss_pred ccHHHHHHHHHhcCCC
Q psy15415 3 LTANLRLFFHRERFPY 18 (128)
Q Consensus 3 LTL~eIY~~I~~~fPy 18 (128)
.++..|..||+++|+.
T Consensus 22 sS~~aI~kyI~~~y~~ 37 (77)
T PF00538_consen 22 SSLQAIKKYIKAKYKV 37 (77)
T ss_dssp EEHHHHHHHHHHHSSC
T ss_pred CCHHHHHHHHHHhcCc
Confidence 3688999999999975
No 19
>PF12990 DUF3874: Domain of unknonw function from B. Theta Gene description (DUF3874); InterPro: IPR024450 This domain of unknown function if found in uncharacterised proteins from Bacteroides thetaiotaomicron and other Bacteroidetes.
Probab=23.88 E-value=56 Score=21.96 Aligned_cols=17 Identities=18% Similarity=-0.001 Sum_probs=15.0
Q ss_pred cccHHHHHHHHHhcCCC
Q psy15415 2 ALTANLRLFFHRERFPY 18 (128)
Q Consensus 2 rLTL~eIY~~I~~~fPy 18 (128)
.||..||++.|.+++|-
T Consensus 25 ~lsa~~If~~L~k~~~~ 41 (73)
T PF12990_consen 25 WLSAAEIFERLQKKSPA 41 (73)
T ss_pred eecHHHHHHHHHHhCcc
Confidence 48899999999999885
Done!