Query psy15601
Match_columns 144
No_of_seqs 147 out of 744
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 16:52:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15601.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15601hhsearch_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 6.8E-32 1.5E-36 189.0 3.3 61 1-61 13-78 (78)
2 PF00250 Fork_head: Fork head 100.0 9.2E-31 2E-35 189.1 1.3 65 1-65 13-82 (96)
3 smart00339 FH FORKHEAD. FORKHE 100.0 3E-30 6.5E-35 184.3 3.3 66 1-66 13-83 (89)
4 KOG3563|consensus 99.9 3.9E-28 8.6E-33 209.7 4.4 78 1-78 185-274 (454)
5 KOG2294|consensus 99.9 9.9E-27 2.2E-31 199.9 1.6 63 1-63 142-211 (454)
6 KOG3562|consensus 99.9 2.2E-26 4.8E-31 188.9 3.2 63 1-63 25-92 (277)
7 KOG4385|consensus 99.9 6.2E-24 1.4E-28 188.6 -1.1 75 1-75 380-454 (581)
8 COG5025 Transcription factor o 99.6 4.5E-17 9.8E-22 148.7 2.1 66 1-66 349-419 (610)
9 COG5025 Transcription factor o 99.2 6.2E-12 1.3E-16 115.3 0.4 64 1-64 98-166 (610)
10 PF05066 HARE-HTH: HB1, ASXL, 65.7 6.8 0.00015 25.9 2.6 47 6-53 14-65 (72)
11 KOG4385|consensus 57.0 3.9 8.4E-05 37.9 0.3 39 33-71 472-510 (581)
12 PF14338 Mrr_N: Mrr N-terminal 48.9 18 0.0004 25.0 2.6 58 6-63 16-83 (92)
13 COG2958 Uncharacterized protei 46.6 10 0.00023 32.7 1.2 59 2-60 14-84 (307)
14 PF00538 Linker_histone: linke 37.5 15 0.00033 24.8 0.7 44 7-51 19-65 (77)
15 PF10826 DUF2551: Protein of u 34.2 34 0.00074 24.5 2.1 18 7-24 23-40 (83)
16 PF12872 OST-HTH: OST-HTH/LOTU 32.8 54 0.0012 21.1 2.8 49 7-56 21-70 (74)
17 PF13592 HTH_33: Winged helix- 29.3 48 0.0011 21.2 2.1 19 7-25 2-20 (60)
18 smart00258 SAND SAND domain. 26.9 23 0.0005 24.7 0.2 15 29-43 48-62 (73)
19 PF06531 DUF1108: Protein of u 26.1 45 0.00098 24.0 1.6 11 12-22 62-72 (86)
20 cd01770 p47_UBX p47-like ubiqu 25.7 53 0.0012 22.5 1.9 15 10-24 25-39 (79)
21 smart00526 H15 Domain in histo 24.5 47 0.001 21.5 1.3 19 7-25 21-39 (66)
22 cd01767 UBX UBX (ubiquitin reg 23.8 57 0.0012 21.6 1.7 14 10-23 23-36 (77)
23 PF01342 SAND: SAND domain; I 22.0 29 0.00062 24.3 -0.1 13 28-40 56-68 (82)
24 PF11927 DUF3445: Protein of u 21.7 62 0.0013 26.8 1.8 33 6-38 41-81 (249)
25 PF10523 BEN: BEN domain; Int 21.4 67 0.0015 20.9 1.6 25 11-39 42-66 (79)
26 PF10264 Stork_head: Winged he 21.0 81 0.0018 22.3 2.0 37 3-42 23-59 (80)
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=6.8e-32 Score=188.96 Aligned_cols=61 Identities=54% Similarity=1.087 Sum_probs=58.9
Q ss_pred CCCCCCCCCcCHHHHHHHHHhhcCCCccccccccccchhhcccCccceeecc-----CCCceEEec
Q psy15601 1 SIIESPDKQLTLNEIYNWFQNTFCYFRRNAATWKNAVRHNLSLHKCFMRVEN-----VKGAVWTVD 61 (144)
Q Consensus 1 AI~~Sp~~~LTL~eIY~~I~~~fPyfr~~~~gWkNSIRHNLS~n~~F~Kv~r-----gkg~~W~i~ 61 (144)
||++||+++|||+|||+||+++||||+.+.+|||||||||||+|+||+||++ |||+||+||
T Consensus 13 Ai~~sp~~~lTL~eIy~~I~~~~pyyr~~~~gWknSIRHnLS~n~~F~kv~r~~~~~gkg~~W~i~ 78 (78)
T cd00059 13 AIQSSPEKRLTLSEIYKWISDNFPYFRDAPAGWQNSIRHNLSLNKCFVKVPREPDEPGKGSYWTLD 78 (78)
T ss_pred HHHhCCCCCeeHHHHHHHHHHhCCccccCCCCCccceeEecccccceEECCCCCCCCCCCCeeeeC
Confidence 7999999999999999999999999999999999999999999999999976 699999997
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=9.2e-31 Score=189.08 Aligned_cols=65 Identities=51% Similarity=1.045 Sum_probs=60.8
Q ss_pred CCCCCCCCCcCHHHHHHHHHhhcCCCccccccccccchhhcccCccceeecc-----CCCceEEecchhh
Q psy15601 1 SIIESPDKQLTLNEIYNWFQNTFCYFRRNAATWKNAVRHNLSLHKCFMRVEN-----VKGAVWTVDEVEF 65 (144)
Q Consensus 1 AI~~Sp~~~LTL~eIY~~I~~~fPyfr~~~~gWkNSIRHNLS~n~~F~Kv~r-----gkg~~W~i~~~~~ 65 (144)
||++||+++|||+|||+||+++||||+.+.++||||||||||+|+||+||++ |||++|+|+++..
T Consensus 13 Ai~~sp~~~Ltl~eIy~~i~~~~pyyr~~~~~WknSIRHnLS~~~~F~kv~~~~~~~gkg~~W~i~~~~~ 82 (96)
T PF00250_consen 13 AILSSPDKRLTLSEIYEWIEENFPYYRDASKGWKNSIRHNLSLNKCFVKVPRDPSEPGKGSYWTIDPEAI 82 (96)
T ss_dssp HHHTSTTSEBEHHHHHHHHHHHCGHHHCTHCHHHHHHHHHHHHSTTEEEESCCTSSSSSSEEEEE-CTHH
T ss_pred HHHhCCCCCccHHHHHHHHHHhhccccccchhhhhHHhhhccccceeeecCcCCCCCCCceeEEeCHHHH
Confidence 7999999999999999999999999999999999999999999999999976 7999999998753
No 3
>smart00339 FH FORKHEAD. FORKHEAD, also known as a "winged helix"
Probab=99.96 E-value=3e-30 Score=184.26 Aligned_cols=66 Identities=50% Similarity=0.999 Sum_probs=62.2
Q ss_pred CCCCCCCCCcCHHHHHHHHHhhcCCCccccccccccchhhcccCccceeecc-----CCCceEEecchhhh
Q psy15601 1 SIIESPDKQLTLNEIYNWFQNTFCYFRRNAATWKNAVRHNLSLHKCFMRVEN-----VKGAVWTVDEVEFY 66 (144)
Q Consensus 1 AI~~Sp~~~LTL~eIY~~I~~~fPyfr~~~~gWkNSIRHNLS~n~~F~Kv~r-----gkg~~W~i~~~~~~ 66 (144)
||++||+++|||+|||+||+++||||+.+.+|||||||||||+|+||+||++ |||++|+|+++...
T Consensus 13 ai~~sp~~~ltl~~Iy~~I~~~~pyy~~~~~~WknSIRHnLS~n~~F~kv~~~~~~~gkg~~W~i~~~~~~ 83 (89)
T smart00339 13 AILSSPDKRLTLSEIYKWIEDNFPYYRENRAGWQNSIRHNLSLNDCFVKVPREGDRPGKGSYWTLDPDAEN 83 (89)
T ss_pred HHHhCCCCCeeHHHHHHHHHHhCchhhcCccccccccccccchhhceeecCcCCCCCCCCCEEEECccHHH
Confidence 7899999999999999999999999999999999999999999999999975 79999999987643
No 4
>KOG3563|consensus
Probab=99.94 E-value=3.9e-28 Score=209.69 Aligned_cols=78 Identities=40% Similarity=0.854 Sum_probs=68.6
Q ss_pred CCCCCCCCCcCHHHHHHHHHhhcCCCccccccccccchhhcccCccceeecc-----CCCceEEecch-------hhhhc
Q psy15601 1 SIIESPDKQLTLNEIYNWFQNTFCYFRRNAATWKNAVRHNLSLHKCFMRVEN-----VKGAVWTVDEV-------EFYKR 68 (144)
Q Consensus 1 AI~~Sp~~~LTL~eIY~~I~~~fPyfr~~~~gWkNSIRHNLS~n~~F~Kv~r-----gkg~~W~i~~~-------~~~~r 68 (144)
||+.+|.++|||.|||+||++.|||||.+...|||||||.||+|+|||||+| |||+||||.|. .++-|
T Consensus 185 AIQ~~pskmLTLSEIYqwIMDLFPyYrqNQQRWQNSIRHSLSFNDCFVKVaRSPDKPGKGSfWTLHpdsGNMFENGCYLR 264 (454)
T KOG3563|consen 185 AIQQAPSKMLTLSEIYQWIMDLFPYYRQNQQRWQNSIRHSLSFNDCFVKVARSPDKPGKGSFWTLHPDSGNMFENGCYLR 264 (454)
T ss_pred HHHhCCccceeHHHHHHHHHHhhhHhhhhHHHHHhhhhhhccccceeeeccCCCCCCCCccceeecCCcCcccccchheh
Confidence 7999999999999999999999999999999999999999999999999976 89999999864 45556
Q ss_pred CccccCCCCc
Q psy15601 69 RPQRMLSGQT 78 (144)
Q Consensus 69 r~~r~~~~~~ 78 (144)
|.+|.+..++
T Consensus 265 RQKRFK~ekk 274 (454)
T KOG3563|consen 265 RQKRFKCEKK 274 (454)
T ss_pred hhhhhhhhhh
Confidence 6555554433
No 5
>KOG2294|consensus
Probab=99.92 E-value=9.9e-27 Score=199.90 Aligned_cols=63 Identities=48% Similarity=0.839 Sum_probs=60.1
Q ss_pred CCCCCCCCCcCHHHHHHHHHh-hcCCCcccc-ccccccchhhcccCccceeecc-----CCCceEEecch
Q psy15601 1 SIIESPDKQLTLNEIYNWFQN-TFCYFRRNA-ATWKNAVRHNLSLHKCFMRVEN-----VKGAVWTVDEV 63 (144)
Q Consensus 1 AI~~Sp~~~LTL~eIY~~I~~-~fPyfr~~~-~gWkNSIRHNLS~n~~F~Kv~r-----gkg~~W~i~~~ 63 (144)
||+.||+|+|||+|||+||.. +||||+.+. .|||||||||||+|+||+||+| |||+||+||++
T Consensus 142 AI~~Sp~krLtLs~Iy~~i~~~~fpyyr~~~~~gWqNSIRHNLSLn~cF~Kvpr~~~~~gKg~~W~ldP~ 211 (454)
T KOG2294|consen 142 AIRLSPGKRLTLGGIYFYILLEHFPYYRDANMPGWKNSIRHNLSLNKCFVKVPRERGRPGKGNYWTLDPD 211 (454)
T ss_pred ccccCCCcceeecCeeEEEEeccccccccCCCccchhhcccccccccCccccCCcccCCCCCCccccCcc
Confidence 899999999999999999995 999999999 9999999999999999999975 79999999974
No 6
>KOG3562|consensus
Probab=99.92 E-value=2.2e-26 Score=188.86 Aligned_cols=63 Identities=38% Similarity=0.898 Sum_probs=61.0
Q ss_pred CCCCCCCCCcCHHHHHHHHHhhcCCCccccccccccchhhcccCccceeecc-----CCCceEEecch
Q psy15601 1 SIIESPDKQLTLNEIYNWFQNTFCYFRRNAATWKNAVRHNLSLHKCFMRVEN-----VKGAVWTVDEV 63 (144)
Q Consensus 1 AI~~Sp~~~LTL~eIY~~I~~~fPyfr~~~~gWkNSIRHNLS~n~~F~Kv~r-----gkg~~W~i~~~ 63 (144)
||.+||+|+|.|.|||.||+++|||||.+...||||+|||||+|+||+||+| |||+||+|.+.
T Consensus 25 AI~~SpekmLPLseIYkfImDrFPfYRkNTQrWQNSLRHNLSFNDCFIKiPRr~drpGKGsyWalHP~ 92 (277)
T KOG3562|consen 25 AIQSSPEKMLPLSEIYKFIMDRFPFYRKNTQRWQNSLRHNLSFNDCFIKIPRRPDRPGKGSYWALHPS 92 (277)
T ss_pred HhhcChhhcCcHHHHHHHHHhhCchhhhchHHHHHHhhccccccceeeecCCCCCCCCCccceeeccc
Confidence 7999999999999999999999999999999999999999999999999986 89999999874
No 7
>KOG4385|consensus
Probab=99.87 E-value=6.2e-24 Score=188.57 Aligned_cols=75 Identities=84% Similarity=1.377 Sum_probs=72.3
Q ss_pred CCCCCCCCCcCHHHHHHHHHhhcCCCccccccccccchhhcccCccceeeccCCCceEEecchhhhhcCccccCC
Q psy15601 1 SIIESPDKQLTLNEIYNWFQNTFCYFRRNAATWKNAVRHNLSLHKCFMRVENVKGAVWTVDEVEFYKRRPQRMLS 75 (144)
Q Consensus 1 AI~~Sp~~~LTL~eIY~~I~~~fPyfr~~~~gWkNSIRHNLS~n~~F~Kv~rgkg~~W~i~~~~~~~rr~~r~~~ 75 (144)
||++|||++|||+|||.|+++.|.|||.+...|||+||||||+++||++|+.-||..|++|+.++.+||+.+...
T Consensus 380 AIlESpdkQLTLNEIY~WFTrtFAYFRRNaATWKnAVRHNLSLHKCF~RVEnvkgavwtvDe~e~~krr~~k~~g 454 (581)
T KOG4385|consen 380 AILESPDKQLTLNEIYNWFTRTFAYFRRNAATWKNAVRHNLSLHKCFVRVENVKGAVWTVDEREFQKRRPQKITG 454 (581)
T ss_pred HHhcCchhhccHHHHHHHHHHHHHHHhccchhHhHHHhhhhHHHHHHHHHHHHhcceeeeehhhhhhhcCccccC
Confidence 799999999999999999999999999999999999999999999999999999999999999999999887653
No 8
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.64 E-value=4.5e-17 Score=148.75 Aligned_cols=66 Identities=41% Similarity=0.893 Sum_probs=62.2
Q ss_pred CCCCCCCCCcCHHHHHHHHHhhcCCCccccccccccchhhcccCccceeecc-----CCCceEEecchhhh
Q psy15601 1 SIIESPDKQLTLNEIYNWFQNTFCYFRRNAATWKNAVRHNLSLHKCFMRVEN-----VKGAVWTVDEVEFY 66 (144)
Q Consensus 1 AI~~Sp~~~LTL~eIY~~I~~~fPyfr~~~~gWkNSIRHNLS~n~~F~Kv~r-----gkg~~W~i~~~~~~ 66 (144)
||+.+|+++|+|.|||.||...||||+....+|+||||||||+|++|.||++ |||+||.++++..+
T Consensus 349 ail~s~~~kmsls~Iy~~i~s~~pyYr~~p~~w~nSiRhnlSlNksf~kvP~sa~~pGKg~fw~i~~s~~~ 419 (610)
T COG5025 349 AILSSPSGKMTLSEIYSWISSNLPYYRHKPTAWQNSIRHNLSLNKSFEKVPRSASQPGKGCFWKIDYSYIY 419 (610)
T ss_pred HhhcCcccccccccccccccccchhhccCCcccCchhhhhhhhccccccCCCCcCCCCCcccCccChhhhh
Confidence 6899999999999999999999999999999999999999999999999986 89999999986543
No 9
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.15 E-value=6.2e-12 Score=115.34 Aligned_cols=64 Identities=45% Similarity=0.998 Sum_probs=60.3
Q ss_pred CCCCCCCCCcCHHHHHHHHHhhcCCCccccccccccchhhcccCccceeecc-----CCCceEEecchh
Q psy15601 1 SIIESPDKQLTLNEIYNWFQNTFCYFRRNAATWKNAVRHNLSLHKCFMRVEN-----VKGAVWTVDEVE 64 (144)
Q Consensus 1 AI~~Sp~~~LTL~eIY~~I~~~fPyfr~~~~gWkNSIRHNLS~n~~F~Kv~r-----gkg~~W~i~~~~ 64 (144)
||+.+++++|||..||.||-..|.||.....+|+|||||||++++.|.|+++ ++|.+|.|.|..
T Consensus 98 ~il~s~~~~lt~s~~~~~~~~~~~~~~k~~~~~~~sIr~Nls~~~a~~~i~g~~g~~~~g~~~~igP~~ 166 (610)
T COG5025 98 AILNSPDKPLTLSKIYTWIHNTFFYYAKVVSRWQNSIRHNLSLNDAFIKIEGRNGAKVKGHFWSIGPGH 166 (610)
T ss_pred ccccCcccCCcccceeeeeeecccccccccchhhhhhhcccccCceEEEEeccCCccccceeeccCCCc
Confidence 6899999999999999999999999999999999999999999999999974 689999999854
No 10
>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=65.68 E-value=6.8 Score=25.93 Aligned_cols=47 Identities=19% Similarity=0.285 Sum_probs=28.8
Q ss_pred CCCCcCHHHHHHHHHhhcCCCccccccccccchhhcc-----cCccceeeccC
Q psy15601 6 PDKQLTLNEIYNWFQNTFCYFRRNAATWKNAVRHNLS-----LHKCFMRVENV 53 (144)
Q Consensus 6 p~~~LTL~eIY~~I~~~fPyfr~~~~gWkNSIRHNLS-----~n~~F~Kv~rg 53 (144)
.++.|+.+||++.|.+.--| ....+...++|+-.|. .+..|++|..+
T Consensus 14 ~~~pm~~~eI~~~i~~~~~~-~~~~k~p~~~i~a~ly~~~~~~d~~F~~vg~~ 65 (72)
T PF05066_consen 14 AGRPMTFKEIWEEIQERGLY-KKSGKTPEATIAAQLYTDIKNEDSRFVKVGPG 65 (72)
T ss_dssp H-S-EEHHHHHHHHHHHHTS----GGGGGHHHH-HHHHHHH-T-SS-EESSSS
T ss_pred cCCCcCHHHHHHHHHHhCCC-CcccCCHHHHHHHHHHHHcccCCCCEEEeCCC
Confidence 45789999999999976544 3336777778874333 45589998633
No 11
>KOG4385|consensus
Probab=57.04 E-value=3.9 Score=37.95 Aligned_cols=39 Identities=26% Similarity=0.307 Sum_probs=34.2
Q ss_pred ccccchhhcccCccceeeccCCCceEEecchhhhhcCcc
Q psy15601 33 WKNAVRHNLSLHKCFMRVENVKGAVWTVDEVEFYKRRPQ 71 (144)
Q Consensus 33 WkNSIRHNLS~n~~F~Kv~rgkg~~W~i~~~~~~~rr~~ 71 (144)
-.++++|+|+.|.||.+++.++|+-|++++.++..++-.
T Consensus 472 ~~a~l~~al~~~~~~lls~a~~~~~~s~~~Le~~~~~~~ 510 (581)
T KOG4385|consen 472 PNAALQAALAENSLPLLSEAGMGNNWSVGELEFAKHEDV 510 (581)
T ss_pred hhHHHHHHhhcCccccccchhccCCcchhhHHHHHHhhc
Confidence 568999999999999999999999999998877665544
No 12
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=48.87 E-value=18 Score=25.01 Aligned_cols=58 Identities=22% Similarity=0.306 Sum_probs=40.1
Q ss_pred CCCCcCHHHHHHHHHhhcCCCcc-------cc---ccccccchhhcccCccceeeccCCCceEEecch
Q psy15601 6 PDKQLTLNEIYNWFQNTFCYFRR-------NA---ATWKNAVRHNLSLHKCFMRVENVKGAVWTVDEV 63 (144)
Q Consensus 6 p~~~LTL~eIY~~I~~~fPyfr~-------~~---~gWkNSIRHNLS~n~~F~Kv~rgkg~~W~i~~~ 63 (144)
-++.++.+||++.|.++|..=.. +. .-|+|.|+=.++--+..--+++.+...|.|.+.
T Consensus 16 ~g~~~~~~ei~~~v~~~~~ls~e~~~~~~~sg~~~~~~~~ri~Wa~~~L~~aGli~~~~rG~~~iT~~ 83 (92)
T PF14338_consen 16 LGGSASRKEIYERVAERFGLSDEERNERLPSGQGYSRFKNRIRWARSYLKKAGLIERPKRGIWRITEK 83 (92)
T ss_pred cCCCcCHHHHHHHHHHHhCCCHHHHHHHcccCCcchhHHHhHHHHHHHHHHCCCccCCCCCceEECHh
Confidence 36889999999999999875321 11 158888886665544444445555558999875
No 13
>COG2958 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.63 E-value=10 Score=32.72 Aligned_cols=59 Identities=19% Similarity=0.130 Sum_probs=42.9
Q ss_pred CCCCCCCCcCHHHHHHHHHhhcCCCc------ccccc------ccccchhhcccCccceeeccCCCceEEe
Q psy15601 2 IIESPDKQLTLNEIYNWFQNTFCYFR------RNAAT------WKNAVRHNLSLHKCFMRVENVKGAVWTV 60 (144)
Q Consensus 2 I~~Sp~~~LTL~eIY~~I~~~fPyfr------~~~~g------WkNSIRHNLS~n~~F~Kv~rgkg~~W~i 60 (144)
++..++..+|..|||+|+.+.||-=. ..++. =--+.|-||-.+.-|.||..+..-||--
T Consensus 14 ~Lq~~~ep~t~~eI~eka~e~~~~~~~~kk~~s~g~tp~q~va~~iy~~~~lq~~~pflKvte~P~~~~lk 84 (307)
T COG2958 14 VLQTSEEPFTAREIAEKAFETFPAECQEKKFDSGGDTPQQLVAEIIYTRPNLQEKHPFLKVTEGPRLYYLK 84 (307)
T ss_pred HHHccCCCCcHHHHHHHHHHhccHHHHHHhhccccccHHHHHHHHHhcCccccccCcccccccCceEEeec
Confidence 34558899999999999999998532 22222 2346678888899999997776666644
No 14
>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=37.52 E-value=15 Score=24.77 Aligned_cols=44 Identities=18% Similarity=0.280 Sum_probs=26.8
Q ss_pred CCCcCHHHHHHHHHhhcCCCccccccccccchhhccc---Cccceeec
Q psy15601 7 DKQLTLNEIYNWFQNTFCYFRRNAATWKNAVRHNLSL---HKCFMRVE 51 (144)
Q Consensus 7 ~~~LTL~eIY~~I~~~fPyfr~~~~gWkNSIRHNLS~---n~~F~Kv~ 51 (144)
.+..+++.|..||+++|+.-. ....-+..|+..|-- +..|+++.
T Consensus 19 r~GsS~~aI~kyI~~~y~~~~-~~~~~~~~l~~aLk~~v~~G~l~~~k 65 (77)
T PF00538_consen 19 RKGSSLQAIKKYIKAKYKVDL-NPANFKSRLKRALKRGVEKGKLVQVK 65 (77)
T ss_dssp SSSEEHHHHHHHHHHHSSCCC-CHTTHHHHHHHHHHHHHHCTSEEECS
T ss_pred CCCCCHHHHHHHHHHhcCcCC-ChHHHHHHHHHHHHHHHHCCcEEeec
Confidence 467999999999999997522 222334444444332 44555554
No 15
>PF10826 DUF2551: Protein of unknown function (DUF2551) ; InterPro: IPR020501 This entry contains proteins with no known function.
Probab=34.21 E-value=34 Score=24.50 Aligned_cols=18 Identities=28% Similarity=0.599 Sum_probs=16.1
Q ss_pred CCCcCHHHHHHHHHhhcC
Q psy15601 7 DKQLTLNEIYNWFQNTFC 24 (144)
Q Consensus 7 ~~~LTL~eIY~~I~~~fP 24 (144)
.+.+|..|||+.+.++|.
T Consensus 23 ~~~~T~~di~e~L~~~f~ 40 (83)
T PF10826_consen 23 GKKFTTDDIYERLKEKFD 40 (83)
T ss_pred CCCeeHHHHHHHHHHHcC
Confidence 578999999999999965
No 16
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=32.79 E-value=54 Score=21.13 Aligned_cols=49 Identities=16% Similarity=0.223 Sum_probs=29.5
Q ss_pred CCCcCHHHHHHHHHhhcCCCccccccccccchhhc-ccCccceeeccCCCc
Q psy15601 7 DKQLTLNEIYNWFQNTFCYFRRNAATWKNAVRHNL-SLHKCFMRVENVKGA 56 (144)
Q Consensus 7 ~~~LTL~eIY~~I~~~fPyfr~~~~gWkNSIRHNL-S~n~~F~Kv~rgkg~ 56 (144)
+|.+.|+++-.++.++||-|....=|.. +++.=| ++-+.|+=..++.|.
T Consensus 21 ~g~v~ls~l~~~~~~~~~~f~~~~yG~~-~l~~ll~~~~~~~~i~~~~~g~ 70 (74)
T PF12872_consen 21 DGWVSLSQLGQEYKKKYPDFDPRDYGFS-SLSELLESLPDVVEIEERQHGG 70 (74)
T ss_dssp TSSEEHHHHHHHHHHHHTT--TCCTTSS-SHHHHHHT-TTTEEEEEEECCC
T ss_pred CceEEHHHHHHHHHHHCCCCCccccCCC-cHHHHHHhCCCeEEEeeeCCCC
Confidence 4589999999999999998886655543 233333 444555444444443
No 17
>PF13592 HTH_33: Winged helix-turn helix
Probab=29.29 E-value=48 Score=21.24 Aligned_cols=19 Identities=26% Similarity=0.417 Sum_probs=16.0
Q ss_pred CCCcCHHHHHHHHHhhcCC
Q psy15601 7 DKQLTLNEIYNWFQNTFCY 25 (144)
Q Consensus 7 ~~~LTL~eIY~~I~~~fPy 25 (144)
++..|+.+|.+||++.|--
T Consensus 2 ~~~wt~~~i~~~I~~~fgv 20 (60)
T PF13592_consen 2 GGRWTLKEIAAYIEEEFGV 20 (60)
T ss_pred CCcccHHHHHHHHHHHHCC
Confidence 5678999999999988853
No 18
>smart00258 SAND SAND domain.
Probab=26.90 E-value=23 Score=24.65 Aligned_cols=15 Identities=27% Similarity=0.510 Sum_probs=11.6
Q ss_pred ccccccccchhhccc
Q psy15601 29 NAATWKNAVRHNLSL 43 (144)
Q Consensus 29 ~~~gWkNSIRHNLS~ 43 (144)
..+.|+-|||+|=++
T Consensus 48 ~~K~WK~sIR~~g~~ 62 (73)
T smart00258 48 KSKDWKRSIRCGGSS 62 (73)
T ss_pred ccCCcchheeECCcc
Confidence 457899999987543
No 19
>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=26.05 E-value=45 Score=24.03 Aligned_cols=11 Identities=27% Similarity=0.869 Sum_probs=9.2
Q ss_pred HHHHHHHHHhh
Q psy15601 12 LNEIYNWFQNT 22 (144)
Q Consensus 12 L~eIY~~I~~~ 22 (144)
.+.||+||+++
T Consensus 62 ~~aiyewIE~n 72 (86)
T PF06531_consen 62 NQAIYEWIEEN 72 (86)
T ss_pred HHHHHHHHHhC
Confidence 57899999975
No 20
>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=25.73 E-value=53 Score=22.45 Aligned_cols=15 Identities=7% Similarity=0.180 Sum_probs=12.5
Q ss_pred cCHHHHHHHHHhhcC
Q psy15601 10 LTLNEIYNWFQNTFC 24 (144)
Q Consensus 10 LTL~eIY~~I~~~fP 24 (144)
-|+.+||+||..+.|
T Consensus 25 ~tv~~l~~~v~~~~~ 39 (79)
T cd01770 25 HRVSDVRDFIVNARP 39 (79)
T ss_pred CcHHHHHHHHHHhCC
Confidence 479999999997654
No 21
>smart00526 H15 Domain in histone families 1 and 5.
Probab=24.51 E-value=47 Score=21.52 Aligned_cols=19 Identities=16% Similarity=0.298 Sum_probs=16.0
Q ss_pred CCCcCHHHHHHHHHhhcCC
Q psy15601 7 DKQLTLNEIYNWFQNTFCY 25 (144)
Q Consensus 7 ~~~LTL~eIY~~I~~~fPy 25 (144)
.+..+++.|..||+++|+.
T Consensus 21 r~GsS~~aI~kyi~~~~~~ 39 (66)
T smart00526 21 RKGSSLQAIKKYIEANYKV 39 (66)
T ss_pred CCCCCHHHHHHHHHHhCCC
Confidence 4668999999999999663
No 22
>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=23.80 E-value=57 Score=21.61 Aligned_cols=14 Identities=7% Similarity=0.261 Sum_probs=11.5
Q ss_pred cCHHHHHHHHHhhc
Q psy15601 10 LTLNEIYNWFQNTF 23 (144)
Q Consensus 10 LTL~eIY~~I~~~f 23 (144)
-||++||+||...-
T Consensus 23 ~tl~~l~~fv~~~~ 36 (77)
T cd01767 23 HKLSDVRDFVESNG 36 (77)
T ss_pred CCHHHHHHHHHHcC
Confidence 48999999998653
No 23
>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=22.04 E-value=29 Score=24.27 Aligned_cols=13 Identities=23% Similarity=0.675 Sum_probs=9.1
Q ss_pred cccccccccchhh
Q psy15601 28 RNAATWKNAVRHN 40 (144)
Q Consensus 28 ~~~~gWkNSIRHN 40 (144)
...+.||.|||++
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 3456799999973
No 24
>PF11927 DUF3445: Protein of unknown function (DUF3445); InterPro: IPR021848 This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 264 to 418 amino acids in length. This protein has a conserved RLP sequence motif. This protein has two completely conserved R residues that may be functionally important.
Probab=21.74 E-value=62 Score=26.85 Aligned_cols=33 Identities=18% Similarity=0.501 Sum_probs=21.0
Q ss_pred CCCCcCHHHHHHHHHh----hcC-CCcccccc---ccccch
Q psy15601 6 PDKQLTLNEIYNWFQN----TFC-YFRRNAAT---WKNAVR 38 (144)
Q Consensus 6 p~~~LTL~eIY~~I~~----~fP-yfr~~~~g---WkNSIR 38 (144)
|+...-..|+|+++.+ +|| +|.....+ |.|.+-
T Consensus 41 p~~~~A~~Ell~~v~~~L~~ryP~~F~~~~~~~~~~~n~~~ 81 (249)
T PF11927_consen 41 PGSEAAVWELLELVLDYLPARYPQYFSLDGDGDRWWHNRLT 81 (249)
T ss_pred ccHHHHHHHHHHHHHHHHHHhCchheEEcCCCceeEEeccC
Confidence 4445555677766655 889 77766555 666554
No 25
>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=21.39 E-value=67 Score=20.92 Aligned_cols=25 Identities=24% Similarity=0.543 Sum_probs=20.2
Q ss_pred CHHHHHHHHHhhcCCCccccccccccchh
Q psy15601 11 TLNEIYNWFQNTFCYFRRNAATWKNAVRH 39 (144)
Q Consensus 11 TL~eIY~~I~~~fPyfr~~~~gWkNSIRH 39 (144)
-|+.|.+++..+||-.. ..|+ .|+.
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 7787 5554
No 26
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=21.02 E-value=81 Score=22.32 Aligned_cols=37 Identities=5% Similarity=0.154 Sum_probs=27.1
Q ss_pred CCCCCCCcCHHHHHHHHHhhcCCCccccccccccchhhcc
Q psy15601 3 IESPDKQLTLNEIYNWFQNTFCYFRRNAATWKNAVRHNLS 42 (144)
Q Consensus 3 ~~Sp~~~LTL~eIY~~I~~~fPyfr~~~~gWkNSIRHNLS 42 (144)
+++.+...|+..|.+++.++||--..-+ +..|++.|.
T Consensus 23 ln~~~~~at~E~l~~~L~~~yp~i~~Ps---~e~l~~~L~ 59 (80)
T PF10264_consen 23 LNAAGQPATQETLREHLRKHYPGIAIPS---QEVLYNTLG 59 (80)
T ss_pred HhccCCcchHHHHHHHHHHhCCCCCCCC---HHHHHHHHH
Confidence 4677888999999999999999765322 345555554
Done!