Query psy13925
Match_columns 344
No_of_seqs 177 out of 817
Neff 3.9
Searched_HMMs 46136
Date Fri Aug 16 23:58:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13925.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13925hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3562|consensus 100.0 1.6E-44 3.6E-49 334.4 8.4 133 1-133 1-134 (277)
2 KOG3563|consensus 100.0 3.6E-40 7.8E-45 321.4 9.1 113 2-114 162-274 (454)
3 PF00250 Fork_head: Fork head 100.0 1E-37 2.2E-42 255.6 3.1 96 13-108 1-96 (96)
4 cd00059 FH Forkhead (FH), also 100.0 2.8E-36 6.1E-41 239.5 7.0 78 13-90 1-78 (78)
5 smart00339 FH FORKHEAD. FORKHE 100.0 2.2E-35 4.8E-40 239.1 7.3 88 13-100 1-88 (89)
6 KOG2294|consensus 100.0 3.3E-34 7.2E-39 279.7 -0.5 103 10-112 127-232 (454)
7 KOG4385|consensus 99.8 9.8E-23 2.1E-27 205.1 0.6 81 10-95 365-445 (581)
8 COG5025 Transcription factor o 99.8 7.1E-20 1.5E-24 190.1 3.4 96 9-104 333-428 (610)
9 COG5025 Transcription factor o 99.4 1.1E-14 2.4E-19 151.8 -0.4 95 8-102 81-175 (610)
10 PF00538 Linker_histone: linke 91.5 0.22 4.7E-06 39.1 3.4 33 17-49 4-37 (77)
11 smart00526 H15 Domain in histo 90.2 0.32 7E-06 36.9 3.2 32 17-48 6-38 (66)
12 cd00073 H15 linker histone 1 a 86.0 1.2 2.5E-05 36.0 4.0 33 17-49 6-39 (88)
13 PF05066 HARE-HTH: HB1, ASXL, 80.8 0.89 1.9E-05 34.9 1.4 57 16-74 1-62 (72)
14 PF14338 Mrr_N: Mrr N-terminal 57.3 9.3 0.0002 30.7 2.5 74 17-95 1-86 (92)
15 KOG4012|consensus 52.0 24 0.00051 34.4 4.7 38 15-52 44-82 (243)
16 COG2958 Uncharacterized protei 37.7 39 0.00086 33.7 3.8 69 17-91 6-86 (307)
17 PF12872 OST-HTH: OST-HTH/LOTU 23.0 64 0.0014 24.1 2.0 53 18-71 6-61 (74)
No 1
>KOG3562|consensus
Probab=100.00 E-value=1.6e-44 Score=334.36 Aligned_cols=133 Identities=77% Similarity=1.352 Sum_probs=126.4
Q ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCccccccccccccccccccccccCCCCC
Q psy13925 1 MPRPCRDTYGDQKPPYSYISLTAMAIWSSPEKMLPLSDIYRFIADRFPYYRRNTQRWQNSLRHNLSFNDCFVKIPRRPDR 80 (344)
Q Consensus 1 ~~r~~R~~~~~~KPPySYa~LIa~AI~sSP~krLTLsEIYewI~~~fPYyr~~~~GWKNSIRHNLSlNk~FvKVpR~~~~ 80 (344)
|||+.|+.|++|||||||+.|.+|||.++|+|+|.|+|||++|+++|||||.+.+.||||+|||||+|+||+||+|..++
T Consensus 1 MPRP~k~sY~dQKPPYSYIsLTaMAI~~SpekmLPLseIYkfImDrFPfYRkNTQrWQNSLRHNLSFNDCFIKiPRr~dr 80 (277)
T KOG3562|consen 1 MPRPGKNSYGDQKPPYSYISLTAMAIQSSPEKMLPLSEIYKFIMDRFPFYRKNTQRWQNSLRHNLSFNDCFIKIPRRPDR 80 (277)
T ss_pred CCCCccccccccCCCceeeehhhHHhhcChhhcCcHHHHHHHHHhhCchhhhchHHHHHHhhccccccceeeecCCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcceEEeCCCchhhcccCccccccccccccc-hhHHHHHHHHHHHHhhhhhc
Q psy13925 81 PGKGAYWALHPNALDMFENGSLLRRRRRFKLMK-SDKDKLENELAALANVNRIY 133 (344)
Q Consensus 81 pGKGs~W~l~pea~~~fe~G~~rRRRrr~k~~k-s~~~~l~eelaala~~~r~~ 133 (344)
+|||+||+|+|.|.+|||+|...|||||++..+ .+++..+.++.+.+++.+..
T Consensus 81 pGKGsyWalHP~a~dMFENGS~LRRrKRFrv~k~~d~d~~n~~l~a~a~~~~v~ 134 (277)
T KOG3562|consen 81 PGKGSYWALHPSAFDMFENGSLLRRRKRFRVLKSDDKDPSNTHLPAMANAAYVA 134 (277)
T ss_pred CCCccceeeccchhhhcccchHHHHhhhhhhccccccCcccccccccccchhee
Confidence 999999999999999999999999999999988 45666777888888877643
No 2
>KOG3563|consensus
Probab=100.00 E-value=3.6e-40 Score=321.43 Aligned_cols=113 Identities=63% Similarity=1.194 Sum_probs=108.1
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCccccccccccccccccccccccCCCCCC
Q psy13925 2 PRPCRDTYGDQKPPYSYISLTAMAIWSSPEKMLPLSDIYRFIADRFPYYRRNTQRWQNSLRHNLSFNDCFVKIPRRPDRP 81 (344)
Q Consensus 2 ~r~~R~~~~~~KPPySYa~LIa~AI~sSP~krLTLsEIYewI~~~fPYyr~~~~GWKNSIRHNLSlNk~FvKVpR~~~~p 81 (344)
|.-.|+.|.+.||||||+.||+|||+.+|.|+|||+|||+||++.|||||.+.+.|||||||.||+|+|||||+|.+|++
T Consensus 162 pktyRRsY~haKPPYSYISLITMAIQ~~pskmLTLSEIYqwIMDLFPyYrqNQQRWQNSIRHSLSFNDCFVKVaRSPDKP 241 (454)
T KOG3563|consen 162 PKTYRRSYTHAKPPYSYISLITMAIQQAPSKMLTLSEIYQWIMDLFPYYRQNQQRWQNSIRHSLSFNDCFVKVARSPDKP 241 (454)
T ss_pred CceeeccccCCCCChhHHHHHHHHHHhCCccceeHHHHHHHHHHhhhHhhhhHHHHHhhhhhhccccceeeeccCCCCCC
Confidence 34567899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcceEEeCCCchhhcccCccccccccccccch
Q psy13925 82 GKGAYWALHPNALDMFENGSLLRRRRRFKLMKS 114 (344)
Q Consensus 82 GKGs~W~l~pea~~~fe~G~~rRRRrr~k~~ks 114 (344)
|||+||+|+|++.+|||+|-+.||+||+|..|+
T Consensus 242 GKGSfWTLHpdsGNMFENGCYLRRQKRFK~ekk 274 (454)
T KOG3563|consen 242 GKGSFWTLHPDSGNMFENGCYLRRQKRFKCEKK 274 (454)
T ss_pred CCccceeecCCcCcccccchhehhhhhhhhhhh
Confidence 999999999999999999999999999986543
No 3
>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=100.00 E-value=1e-37 Score=255.55 Aligned_cols=96 Identities=59% Similarity=1.199 Sum_probs=90.3
Q ss_pred CCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCccccccccccccccccccccccCCCCCCCCcceEEeCCC
Q psy13925 13 KPPYSYISLTAMAIWSSPEKMLPLSDIYRFIADRFPYYRRNTQRWQNSLRHNLSFNDCFVKIPRRPDRPGKGAYWALHPN 92 (344)
Q Consensus 13 KPPySYa~LIa~AI~sSP~krLTLsEIYewI~~~fPYyr~~~~GWKNSIRHNLSlNk~FvKVpR~~~~pGKGs~W~l~pe 92 (344)
||||||++||++||+++|+++|||+|||+||+++||||+.+.+|||||||||||+|+||+||+|..++.|||+||+|+++
T Consensus 1 KPp~sY~~LI~~Ai~~sp~~~Ltl~eIy~~i~~~~pyyr~~~~~WknSIRHnLS~~~~F~kv~~~~~~~gkg~~W~i~~~ 80 (96)
T PF00250_consen 1 KPPYSYATLIAMAILSSPDKRLTLSEIYEWIEENFPYYRDASKGWKNSIRHNLSLNKCFVKVPRDPSEPGKGSYWTIDPE 80 (96)
T ss_dssp -SSS-HHHHHHHHHHTSTTSEBEHHHHHHHHHHHCGHHHCTHCHHHHHHHHHHHHSTTEEEESCCTSSSSSSEEEEE-CT
T ss_pred CCCCcHHHHHHHHHHhCCCCCccHHHHHHHHHHhhccccccchhhhhHHhhhccccceeeecCcCCCCCCCceeEEeCHH
Confidence 89999999999999999999999999999999999999999999999999999999999999998888899999999999
Q ss_pred chhhcccCcccccccc
Q psy13925 93 ALDMFENGSLLRRRRR 108 (344)
Q Consensus 93 a~~~fe~G~~rRRRrr 108 (344)
+...|++|.++++|||
T Consensus 81 ~~~~~~~~~~~~~~~~ 96 (96)
T PF00250_consen 81 AIEEFEKGRFKRRRKR 96 (96)
T ss_dssp HHHHHHHSCCSSSSSS
T ss_pred HHHHHhcchhhhhhcc
Confidence 9999999999988875
No 4
>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=100.00 E-value=2.8e-36 Score=239.50 Aligned_cols=78 Identities=67% Similarity=1.265 Sum_probs=76.6
Q ss_pred CCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCccccccccccccccccccccccCCCCCCCCcceEEeC
Q psy13925 13 KPPYSYISLTAMAIWSSPEKMLPLSDIYRFIADRFPYYRRNTQRWQNSLRHNLSFNDCFVKIPRRPDRPGKGAYWALH 90 (344)
Q Consensus 13 KPPySYa~LIa~AI~sSP~krLTLsEIYewI~~~fPYyr~~~~GWKNSIRHNLSlNk~FvKVpR~~~~pGKGs~W~l~ 90 (344)
||||||++||++||+++|+++|||+|||+||+++|||||.+.+|||||||||||+|+||+||+|..+++|||+||+||
T Consensus 1 kP~~sY~~LI~~Ai~~sp~~~lTL~eIy~~I~~~~pyyr~~~~gWknSIRHnLS~n~~F~kv~r~~~~~gkg~~W~i~ 78 (78)
T cd00059 1 KPPYSYSALIAMAIQSSPEKRLTLSEIYKWISDNFPYFRDAPAGWQNSIRHNLSLNKCFVKVPREPDEPGKGSYWTLD 78 (78)
T ss_pred CCCCCHHHHHHHHHHhCCCCCeeHHHHHHHHHHhCCccccCCCCCccceeEecccccceEECCCCCCCCCCCCeeeeC
Confidence 899999999999999999999999999999999999999999999999999999999999999999889999999996
No 5
>smart00339 FH FORKHEAD. FORKHEAD, also known as a "winged helix"
Probab=100.00 E-value=2.2e-35 Score=239.06 Aligned_cols=88 Identities=70% Similarity=1.308 Sum_probs=83.5
Q ss_pred CCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCccccccccccccccccccccccCCCCCCCCcceEEeCCC
Q psy13925 13 KPPYSYISLTAMAIWSSPEKMLPLSDIYRFIADRFPYYRRNTQRWQNSLRHNLSFNDCFVKIPRRPDRPGKGAYWALHPN 92 (344)
Q Consensus 13 KPPySYa~LIa~AI~sSP~krLTLsEIYewI~~~fPYyr~~~~GWKNSIRHNLSlNk~FvKVpR~~~~pGKGs~W~l~pe 92 (344)
||||||++||++||+++|+++|||+|||+||+++|||||.+.+|||||||||||+|+||+||+|..+.+|||+||+|+++
T Consensus 1 kP~~sY~~lI~~ai~~sp~~~ltl~~Iy~~I~~~~pyy~~~~~~WknSIRHnLS~n~~F~kv~~~~~~~gkg~~W~i~~~ 80 (89)
T smart00339 1 KPPYSYIALIAMAILSSPDKRLTLSEIYKWIEDNFPYYRENRAGWQNSIRHNLSLNDCFVKVPREGDRPGKGSYWTLDPD 80 (89)
T ss_pred CCCCCHHHHHHHHHHhCCCCCeeHHHHHHHHHHhCchhhcCccccccccccccchhhceeecCcCCCCCCCCCEEEECcc
Confidence 89999999999999999999999999999999999999999999999999999999999999998888899999999999
Q ss_pred chhhcccC
Q psy13925 93 ALDMFENG 100 (344)
Q Consensus 93 a~~~fe~G 100 (344)
+..+|+.+
T Consensus 81 ~~~~~~~~ 88 (89)
T smart00339 81 AENMFENG 88 (89)
T ss_pred HHHHHhcC
Confidence 98755543
No 6
>KOG2294|consensus
Probab=99.98 E-value=3.3e-34 Score=279.69 Aligned_cols=103 Identities=55% Similarity=0.982 Sum_probs=96.9
Q ss_pred CCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHh-cCCCcccCc-cccccccccccccccccccccCCCCCCCCcceE
Q psy13925 10 GDQKPPYSYISLTAMAIWSSPEKMLPLSDIYRFIAD-RFPYYRRNT-QRWQNSLRHNLSFNDCFVKIPRRPDRPGKGAYW 87 (344)
Q Consensus 10 ~~~KPPySYa~LIa~AI~sSP~krLTLsEIYewI~~-~fPYyr~~~-~GWKNSIRHNLSlNk~FvKVpR~~~~pGKGs~W 87 (344)
..+||||||++||+|||+.+|+|+|||+|||+||+. +|||||++. .|||||||||||||+||+||+|..+++|||+||
T Consensus 127 ~~~kpp~SY~~LI~mAI~~Sp~krLtLs~Iy~~i~~~~fpyyr~~~~~gWqNSIRHNLSLn~cF~Kvpr~~~~~gKg~~W 206 (454)
T KOG2294|consen 127 AGVKPPYSYSGLIAMAIRLSPGKRLTLGGIYFYILLEHFPYYRDANMPGWKNSIRHNLSLNKCFVKVPRERGRPGKGNYW 206 (454)
T ss_pred CCcCCccccccccccccccCCCcceeecCeeEEEEeccccccccCCCccchhhcccccccccCccccCCcccCCCCCCcc
Confidence 468999999999999999999999999999999995 999999999 999999999999999999999988889999999
Q ss_pred EeCCCchh-hcccCcccccccccccc
Q psy13925 88 ALHPNALD-MFENGSLLRRRRRFKLM 112 (344)
Q Consensus 88 ~l~pea~~-~fe~G~~rRRRrr~k~~ 112 (344)
+|+|++.+ +|++|.++|||++.+..
T Consensus 207 ~ldP~~~~~~~~~g~~~rr~~~~~~~ 232 (454)
T KOG2294|consen 207 TLDPDDENNMFDNGSFRRRRRSKSNG 232 (454)
T ss_pred ccCcchhccccccccccccccccccc
Confidence 99999999 99999998888875543
No 7
>KOG4385|consensus
Probab=99.85 E-value=9.8e-23 Score=205.06 Aligned_cols=81 Identities=42% Similarity=0.920 Sum_probs=76.4
Q ss_pred CCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCccccccccccccccccccccccCCCCCCCCcceEEe
Q psy13925 10 GDQKPPYSYISLTAMAIWSSPEKMLPLSDIYRFIADRFPYYRRNTQRWQNSLRHNLSFNDCFVKIPRRPDRPGKGAYWAL 89 (344)
Q Consensus 10 ~~~KPPySYa~LIa~AI~sSP~krLTLsEIYewI~~~fPYyr~~~~GWKNSIRHNLSlNk~FvKVpR~~~~pGKGs~W~l 89 (344)
.|.+|||+|+.||.+||+++|++.|||+|||.|+.+.|.|||.+...|||+||||||+++||++|+. -||.-|++
T Consensus 365 ~dvRPPfTYAsLIRqAIlESpdkQLTLNEIY~WFTrtFAYFRRNaATWKnAVRHNLSLHKCF~RVEn-----vkgavwtv 439 (581)
T KOG4385|consen 365 ADVRPPFTYASLIRQAILESPDKQLTLNEIYNWFTRTFAYFRRNAATWKNAVRHNLSLHKCFVRVEN-----VKGAVWTV 439 (581)
T ss_pred cccCCchhHHHHHHHHHhcCchhhccHHHHHHHHHHHHHHHhccchhHhHHHhhhhHHHHHHHHHHH-----Hhcceeee
Confidence 4899999999999999999999999999999999999999999999999999999999999999953 69999999
Q ss_pred CCCchh
Q psy13925 90 HPNALD 95 (344)
Q Consensus 90 ~pea~~ 95 (344)
|.....
T Consensus 440 De~e~~ 445 (581)
T KOG4385|consen 440 DEREFQ 445 (581)
T ss_pred ehhhhh
Confidence 987653
No 8
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.78 E-value=7.1e-20 Score=190.09 Aligned_cols=96 Identities=41% Similarity=0.758 Sum_probs=89.0
Q ss_pred CCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCccccccccccccccccccccccCCCCCCCCcceEE
Q psy13925 9 YGDQKPPYSYISLTAMAIWSSPEKMLPLSDIYRFIADRFPYYRRNTQRWQNSLRHNLSFNDCFVKIPRRPDRPGKGAYWA 88 (344)
Q Consensus 9 ~~~~KPPySYa~LIa~AI~sSP~krLTLsEIYewI~~~fPYyr~~~~GWKNSIRHNLSlNk~FvKVpR~~~~pGKGs~W~ 88 (344)
....||+++|+.||+.||+.++.++|+|.+||.||..+|||||....+||||||||||+|++|.||+|...++|||+||.
T Consensus 333 ~~~~kP~~sya~~iT~ail~s~~~kmsls~Iy~~i~s~~pyYr~~p~~w~nSiRhnlSlNksf~kvP~sa~~pGKg~fw~ 412 (610)
T COG5025 333 NRTSKPAFSYANSITQAILSSPSGKMTLSEIYSWISSNLPYYRHKPTAWQNSIRHNLSLNKSFEKVPRSASQPGKGCFWK 412 (610)
T ss_pred ccCccCCcchhhhhHHHhhcCcccccccccccccccccchhhccCCcccCchhhhhhhhccccccCCCCcCCCCCcccCc
Confidence 45789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eCCCchhhcccCcccc
Q psy13925 89 LHPNALDMFENGSLLR 104 (344)
Q Consensus 89 l~pea~~~fe~G~~rR 104 (344)
++.+..+.++.-..++
T Consensus 413 i~~s~~~~~~sk~~~~ 428 (610)
T COG5025 413 IDYSYIYEKESKRNPR 428 (610)
T ss_pred cChhhhhhhccccccc
Confidence 9999998665443333
No 9
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.44 E-value=1.1e-14 Score=151.76 Aligned_cols=95 Identities=43% Similarity=0.775 Sum_probs=88.0
Q ss_pred CCCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCccccccccccccccccccccccCCCCCCCCcceE
Q psy13925 8 TYGDQKPPYSYISLTAMAIWSSPEKMLPLSDIYRFIADRFPYYRRNTQRWQNSLRHNLSFNDCFVKIPRRPDRPGKGAYW 87 (344)
Q Consensus 8 ~~~~~KPPySYa~LIa~AI~sSP~krLTLsEIYewI~~~fPYyr~~~~GWKNSIRHNLSlNk~FvKVpR~~~~pGKGs~W 87 (344)
.|.--||||+|+.+|.++|..+++++|||..||.||...|.||.....+|+|+|||||+++++|.|+.+..+-.+||+||
T Consensus 81 ~~t~~v~~~s~a~gr~~~il~s~~~~lt~s~~~~~~~~~~~~~~k~~~~~~~sIr~Nls~~~a~~~i~g~~g~~~~g~~~ 160 (610)
T COG5025 81 NWTYYVPPYSYATGRGLAILNSPDKPLTLSKIYTWIHNTFFYYAKVVSRWQNSIRHNLSLNDAFIKIEGRNGAKVKGHFW 160 (610)
T ss_pred CcccccCCeeeeeccccccccCcccCCcccceeeeeeecccccccccchhhhhhhcccccCceEEEEeccCCccccceee
Confidence 34557999999999999999999999999999999999999999999999999999999999999999998888999999
Q ss_pred EeCCCchhhcccCcc
Q psy13925 88 ALHPNALDMFENGSL 102 (344)
Q Consensus 88 ~l~pea~~~fe~G~~ 102 (344)
.+.|+....|..+..
T Consensus 161 ~igP~~~~~~l~~g~ 175 (610)
T COG5025 161 SIGPGHETQFLKSGL 175 (610)
T ss_pred ccCCCccceeecccc
Confidence 999998877755544
No 10
>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=91.53 E-value=0.22 Score=39.11 Aligned_cols=33 Identities=24% Similarity=0.323 Sum_probs=29.3
Q ss_pred CHHHHHHHHHhcCCC-CCCCHHHHHHHHHhcCCC
Q psy13925 17 SYISLTAMAIWSSPE-KMLPLSDIYRFIADRFPY 49 (344)
Q Consensus 17 SYa~LIa~AI~sSP~-krLTLsEIYewI~~~fPY 49 (344)
+|.+||..||.+..+ +..++..|..||+++|+.
T Consensus 4 ~y~~mI~eAI~~l~er~GsS~~aI~kyI~~~y~~ 37 (77)
T PF00538_consen 4 PYSDMILEAIKALKERKGSSLQAIKKYIKAKYKV 37 (77)
T ss_dssp CHHHHHHHHHHHCCSSSSEEHHHHHHHHHHHSSC
T ss_pred CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcCc
Confidence 799999999997554 889999999999999964
No 11
>smart00526 H15 Domain in histone families 1 and 5.
Probab=90.21 E-value=0.32 Score=36.89 Aligned_cols=32 Identities=25% Similarity=0.341 Sum_probs=28.3
Q ss_pred CHHHHHHHHHhcCCC-CCCCHHHHHHHHHhcCC
Q psy13925 17 SYISLTAMAIWSSPE-KMLPLSDIYRFIADRFP 48 (344)
Q Consensus 17 SYa~LIa~AI~sSP~-krLTLsEIYewI~~~fP 48 (344)
+|..||..||.+..+ +..+.+.|..||+++|+
T Consensus 6 ~~~~mI~eAI~~l~er~GsS~~aI~kyi~~~~~ 38 (66)
T smart00526 6 PYSEMITEAISALKERKGSSLQAIKKYIEANYK 38 (66)
T ss_pred CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCC
Confidence 899999999997654 66899999999999965
No 12
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=85.96 E-value=1.2 Score=36.05 Aligned_cols=33 Identities=21% Similarity=0.339 Sum_probs=28.9
Q ss_pred CHHHHHHHHHhc-CCCCCCCHHHHHHHHHhcCCC
Q psy13925 17 SYISLTAMAIWS-SPEKMLPLSDIYRFIADRFPY 49 (344)
Q Consensus 17 SYa~LIa~AI~s-SP~krLTLsEIYewI~~~fPY 49 (344)
+|..||..||.. ...+..++..|..||+++|+.
T Consensus 6 ~y~~MI~eAI~~l~er~GsS~~aI~kyI~~~y~~ 39 (88)
T cd00073 6 PYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKV 39 (88)
T ss_pred CHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCc
Confidence 899999999986 446778999999999999874
No 13
>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=80.76 E-value=0.89 Score=34.89 Aligned_cols=57 Identities=14% Similarity=0.259 Sum_probs=36.7
Q ss_pred CCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCccccccccccccc-----cccccccc
Q psy13925 16 YSYISLTAMAIWSSPEKMLPLSDIYRFIADRFPYYRRNTQRWQNSLRHNLS-----FNDCFVKI 74 (344)
Q Consensus 16 ySYa~LIa~AI~sSP~krLTLsEIYewI~~~fPYyr~~~~GWKNSIRHNLS-----lNk~FvKV 74 (344)
+||..++...|+... +-|+.+||++.|.+.--| ...++...++|+-.|. .+..|++|
T Consensus 1 mt~~eaa~~vL~~~~-~pm~~~eI~~~i~~~~~~-~~~~k~p~~~i~a~ly~~~~~~d~~F~~v 62 (72)
T PF05066_consen 1 MTFKEAAYEVLEEAG-RPMTFKEIWEEIQERGLY-KKSGKTPEATIAAQLYTDIKNEDSRFVKV 62 (72)
T ss_dssp S-HHHHHHHHHHHH--S-EEHHHHHHHHHHHHTS----GGGGGHHHH-HHHHHHH-T-SS-EES
T ss_pred CCHHHHHHHHHHhcC-CCcCHHHHHHHHHHhCCC-CcccCCHHHHHHHHHHHHcccCCCCEEEe
Confidence 367788888887777 888999999999976543 3336677778874443 44589988
No 14
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=57.27 E-value=9.3 Score=30.69 Aligned_cols=74 Identities=22% Similarity=0.333 Sum_probs=46.0
Q ss_pred CHHHHHHHHHh--cCCCCCCCHHHHHHHHHhcCCCc--------ccCcc--ccccccccccccccccccccCCCCCCCCc
Q psy13925 17 SYISLTAMAIW--SSPEKMLPLSDIYRFIADRFPYY--------RRNTQ--RWQNSLRHNLSFNDCFVKIPRRPDRPGKG 84 (344)
Q Consensus 17 SYa~LIa~AI~--sSP~krLTLsEIYewI~~~fPYy--------r~~~~--GWKNSIRHNLSlNk~FvKVpR~~~~pGKG 84 (344)
+|..|+...|. ..-++.++.+||++.|.++|..= ..+.. .|+|.|+=.++-=+..--+. .+++|
T Consensus 1 ~~~~~~~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~~~~~~~sg~~~~~~~~ri~Wa~~~L~~aGli~----~~~rG 76 (92)
T PF14338_consen 1 TYDELMPPILEALKDLGGSASRKEIYERVAERFGLSDEERNERLPSGQGYSRFKNRIRWARSYLKKAGLIE----RPKRG 76 (92)
T ss_pred CHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHhCCCHHHHHHHcccCCcchhHHHhHHHHHHHHHHCCCcc----CCCCC
Confidence 46666665544 34468889999999999988743 11111 58888886655433333332 23333
Q ss_pred ceEEeCCCchh
Q psy13925 85 AYWALHPNALD 95 (344)
Q Consensus 85 s~W~l~pea~~ 95 (344)
.|.|.+....
T Consensus 77 -~~~iT~~G~~ 86 (92)
T PF14338_consen 77 -IWRITEKGRK 86 (92)
T ss_pred -ceEECHhHHH
Confidence 9999876543
No 15
>KOG4012|consensus
Probab=51.97 E-value=24 Score=34.37 Aligned_cols=38 Identities=24% Similarity=0.244 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHhcCC-CCCCCHHHHHHHHHhcCCCccc
Q psy13925 15 PYSYISLTAMAIWSSP-EKMLPLSDIYRFIADRFPYYRR 52 (344)
Q Consensus 15 PySYa~LIa~AI~sSP-~krLTLsEIYewI~~~fPYyr~ 52 (344)
.-+|..||..||...- .....+.-|+.+|..+|+.|.-
T Consensus 44 ~P~~~~mi~eAi~a~keR~GsS~aAikK~i~~~Y~g~~v 82 (243)
T KOG4012|consen 44 HPPYSEMITEAISALKERKGSSLAAIKKYIAANYPGDDV 82 (243)
T ss_pred CCcHHHHHHHHHHHhhhcccchHHHHHHHHhhcCccchh
Confidence 4489999999999754 5678999999999999987753
No 16
>COG2958 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.69 E-value=39 Score=33.68 Aligned_cols=69 Identities=17% Similarity=0.205 Sum_probs=45.6
Q ss_pred CHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCc------ccCccc------cccccccccccccccccccCCCCCCCCc
Q psy13925 17 SYISLTAMAIWSSPEKMLPLSDIYRFIADRFPYY------RRNTQR------WQNSLRHNLSFNDCFVKIPRRPDRPGKG 84 (344)
Q Consensus 17 SYa~LIa~AI~sSP~krLTLsEIYewI~~~fPYy------r~~~~G------WKNSIRHNLSlNk~FvKVpR~~~~pGKG 84 (344)
+|..+|-..++ ..+..+|..|||+|+.+.||-= ...++. =--+.|-||-.+--|.||. -|..
T Consensus 6 ~~~e~vl~~Lq-~~~ep~t~~eI~eka~e~~~~~~~~kk~~s~g~tp~q~va~~iy~~~~lq~~~pflKvt-----e~P~ 79 (307)
T COG2958 6 NLIEIVLSVLQ-TSEEPFTAREIAEKAFETFPAECQEKKFDSGGDTPQQLVAEIIYTRPNLQEKHPFLKVT-----EGPR 79 (307)
T ss_pred hhHHHHHHHHH-ccCCCCcHHHHHHHHHHhccHHHHHHhhccccccHHHHHHHHHhcCccccccCcccccc-----cCce
Confidence 45555544444 4999999999999999999832 222222 2245677888888999983 2355
Q ss_pred ceEEeCC
Q psy13925 85 AYWALHP 91 (344)
Q Consensus 85 s~W~l~p 91 (344)
-||.-..
T Consensus 80 ~~~lke~ 86 (307)
T COG2958 80 LYYLKEA 86 (307)
T ss_pred EEeeccc
Confidence 6775543
No 17
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=22.96 E-value=64 Score=24.15 Aligned_cols=53 Identities=19% Similarity=0.230 Sum_probs=34.2
Q ss_pred HHHHHHHHHhcCC--CCCCCHHHHHHHHHhcCCCcccCcccccccccccc-cccccc
Q psy13925 18 YISLTAMAIWSSP--EKMLPLSDIYRFIADRFPYYRRNTQRWQNSLRHNL-SFNDCF 71 (344)
Q Consensus 18 Ya~LIa~AI~sSP--~krLTLsEIYewI~~~fPYyr~~~~GWKNSIRHNL-SlNk~F 71 (344)
-..+|..+|.+.+ ++.+.++++-.++.+++|-|....=|.. ++++-| ++-+.|
T Consensus 6 ~~~~l~~ll~~~~~~~g~v~ls~l~~~~~~~~~~f~~~~yG~~-~l~~ll~~~~~~~ 61 (74)
T PF12872_consen 6 LKKLLRELLESQKGEDGWVSLSQLGQEYKKKYPDFDPRDYGFS-SLSELLESLPDVV 61 (74)
T ss_dssp HHHHHHHHHHHTCTTTSSEEHHHHHHHHHHHHTT--TCCTTSS-SHHHHHHT-TTTE
T ss_pred HHHHHHHHHHhCcCCCceEEHHHHHHHHHHHCCCCCccccCCC-cHHHHHHhCCCeE
Confidence 4567888885554 3579999999999999988876555543 344444 334444
Done!