Query psy15918
Match_columns 376
No_of_seqs 224 out of 838
Neff 3.9
Searched_HMMs 46136
Date Fri Aug 16 16:29:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15918.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15918hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00250 Fork_head: Fork head 100.0 5.4E-38 1.2E-42 260.0 4.6 96 117-212 1-96 (96)
2 cd00059 FH Forkhead (FH), also 100.0 3.6E-37 7.9E-42 247.2 7.9 78 117-194 1-78 (78)
3 smart00339 FH FORKHEAD. FORKHE 100.0 4.2E-36 9.2E-41 245.9 7.9 87 117-203 1-87 (89)
4 KOG3563|consensus 100.0 9.1E-36 2E-40 293.5 7.3 101 113-215 169-269 (454)
5 KOG3562|consensus 100.0 8.6E-35 1.9E-39 272.4 6.6 101 113-213 9-109 (277)
6 KOG2294|consensus 100.0 2.2E-35 4.7E-40 291.3 -1.4 100 113-212 126-228 (454)
7 KOG4385|consensus 99.9 3.6E-23 7.7E-28 210.2 2.9 83 111-198 362-444 (581)
8 COG5025 Transcription factor o 99.8 3.4E-21 7.4E-26 202.0 6.6 97 107-203 327-423 (610)
9 COG5025 Transcription factor o 99.5 2.6E-15 5.6E-20 158.1 -0.1 91 113-203 82-172 (610)
10 PF00538 Linker_histone: linke 93.0 0.14 3E-06 40.7 3.9 33 121-153 4-37 (77)
11 smart00526 H15 Domain in histo 92.1 0.15 3.3E-06 39.2 3.0 32 121-152 6-38 (66)
12 cd00073 H15 linker histone 1 a 88.9 0.65 1.4E-05 37.9 4.2 55 121-178 6-64 (88)
13 PF05066 HARE-HTH: HB1, ASXL, 88.3 0.4 8.7E-06 37.3 2.5 57 120-178 1-62 (72)
14 KOG4012|consensus 69.3 4.5 9.8E-05 39.7 3.2 66 119-194 44-115 (243)
15 PF14338 Mrr_N: Mrr N-terminal 66.1 4.4 9.5E-05 33.0 2.1 73 121-198 1-85 (92)
16 KOG1924|consensus 58.1 38 0.00081 38.9 7.9 8 122-129 424-431 (1102)
17 KOG1528|consensus 43.8 8.5 0.00018 39.3 0.3 38 167-210 109-147 (351)
18 COG2958 Uncharacterized protei 43.3 30 0.00064 34.9 3.9 71 121-197 6-88 (307)
19 PF12872 OST-HTH: OST-HTH/LOTU 37.0 37 0.00081 25.8 2.9 54 122-176 6-62 (74)
20 cd06649 PKc_MEK2 Catalytic dom 24.7 43 0.00093 31.9 1.6 49 122-175 277-328 (331)
No 1
>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=5.4e-38 Score=260.03 Aligned_cols=96 Identities=60% Similarity=1.112 Sum_probs=87.7
Q ss_pred CCCCCHHHHHHHHHhcCCCCCcCHHHHHHHHHhhCCCcccCCCCcccccccccccCcceeeecCCCCCCCCceeeEecCC
Q psy15918 117 KPPYSYNALIMMAIRQSPEKRLTLNGIYEYIMTNFPYYKTNKQGWQNSIRHNLSLNKCFVKVPRHYDDPGKGNYWMLDAS 196 (376)
Q Consensus 117 KPPySYaaLIa~AI~sSp~krLTL~EIY~wI~~~fPYyr~~~~GWqNSIRHNLSLNkcFvKvpR~~~epGKG~~W~ldP~ 196 (376)
||||||++||++||+++++++|||+|||+||+++||||+.+..|||||||||||+|+||+||++..++.|||+||+||++
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 79999999999999999999999999999999999999999999999999999999999999998888899999999999
Q ss_pred chhhhcCCccCccCCC
Q psy15918 197 SEDVFIGGTTGKLRRR 212 (376)
Q Consensus 197 ~e~~f~~G~~~K~RRR 212 (376)
+...|.++...++|+|
T Consensus 81 ~~~~~~~~~~~~~~~~ 96 (96)
T PF00250_consen 81 AIEEFEKGRFKRRRKR 96 (96)
T ss_dssp HHHHHHHSCCSSSSSS
T ss_pred HHHHHhcchhhhhhcc
Confidence 9999999876555443
No 2
>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=3.6e-37 Score=247.22 Aligned_cols=78 Identities=73% Similarity=1.320 Sum_probs=76.8
Q ss_pred CCCCCHHHHHHHHHhcCCCCCcCHHHHHHHHHhhCCCcccCCCCcccccccccccCcceeeecCCCCCCCCceeeEec
Q psy15918 117 KPPYSYNALIMMAIRQSPEKRLTLNGIYEYIMTNFPYYKTNKQGWQNSIRHNLSLNKCFVKVPRHYDDPGKGNYWMLD 194 (376)
Q Consensus 117 KPPySYaaLIa~AI~sSp~krLTL~EIY~wI~~~fPYyr~~~~GWqNSIRHNLSLNkcFvKvpR~~~epGKG~~W~ld 194 (376)
||||||++||++||+++++++|||+|||+||+++|||||.+..|||||||||||+|+||+||+|..+++|||+||+||
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 899999999999999999999999999999999999999999999999999999999999999999889999999997
No 3
>smart00339 FH FORKHEAD. FORKHEAD, also known as a "winged helix"
Probab=100.00 E-value=4.2e-36 Score=245.89 Aligned_cols=87 Identities=68% Similarity=1.216 Sum_probs=83.3
Q ss_pred CCCCCHHHHHHHHHhcCCCCCcCHHHHHHHHHhhCCCcccCCCCcccccccccccCcceeeecCCCCCCCCceeeEecCC
Q psy15918 117 KPPYSYNALIMMAIRQSPEKRLTLNGIYEYIMTNFPYYKTNKQGWQNSIRHNLSLNKCFVKVPRHYDDPGKGNYWMLDAS 196 (376)
Q Consensus 117 KPPySYaaLIa~AI~sSp~krLTL~EIY~wI~~~fPYyr~~~~GWqNSIRHNLSLNkcFvKvpR~~~epGKG~~W~ldP~ 196 (376)
||||||++||++||+++++++|||+|||+||+++|||||.+..|||||||||||+|+||+||+|..+.+|||+||+|+++
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 79999999999999999999999999999999999999999999999999999999999999998888899999999999
Q ss_pred chhhhcC
Q psy15918 197 SEDVFIG 203 (376)
Q Consensus 197 ~e~~f~~ 203 (376)
++.+|..
T Consensus 81 ~~~~~~~ 87 (89)
T smart00339 81 AENMFEN 87 (89)
T ss_pred HHHHHhc
Confidence 9886653
No 4
>KOG3563|consensus
Probab=100.00 E-value=9.1e-36 Score=293.50 Aligned_cols=101 Identities=55% Similarity=0.992 Sum_probs=95.5
Q ss_pred CCCCCCCCCHHHHHHHHHhcCCCCCcCHHHHHHHHHhhCCCcccCCCCcccccccccccCcceeeecCCCCCCCCceeeE
Q psy15918 113 KKDEKPPYSYNALIMMAIRQSPEKRLTLNGIYEYIMTNFPYYKTNKQGWQNSIRHNLSLNKCFVKVPRHYDDPGKGNYWM 192 (376)
Q Consensus 113 k~~~KPPySYaaLIa~AI~sSp~krLTL~EIY~wI~~~fPYyr~~~~GWqNSIRHNLSLNkcFvKvpR~~~epGKG~~W~ 192 (376)
-...||||||+.||.|||+.++.|+|||+|||+||++-|||||.+...|||||||.||+|+|||||+|..+.+|||+||+
T Consensus 169 Y~haKPPYSYISLITMAIQ~~pskmLTLSEIYqwIMDLFPyYrqNQQRWQNSIRHSLSFNDCFVKVaRSPDKPGKGSfWT 248 (454)
T KOG3563|consen 169 YTHAKPPYSYISLITMAIQQAPSKMLTLSEIYQWIMDLFPYYRQNQQRWQNSIRHSLSFNDCFVKVARSPDKPGKGSFWT 248 (454)
T ss_pred ccCCCCChhHHHHHHHHHHhCCccceeHHHHHHHHHHhhhHhhhhHHHHHhhhhhhccccceeeeccCCCCCCCCcccee
Confidence 34789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCchhhhcCCccCccCCCChh
Q psy15918 193 LDASSEDVFIGGTTGKLRRRTTA 215 (376)
Q Consensus 193 ldP~~e~~f~~G~~~K~RRR~~a 215 (376)
|.|++-++|++|-. +||+|+-
T Consensus 249 LHpdsGNMFENGCY--LRRQKRF 269 (454)
T KOG3563|consen 249 LHPDSGNMFENGCY--LRRQKRF 269 (454)
T ss_pred ecCCcCcccccchh--ehhhhhh
Confidence 99999999999975 5665543
No 5
>KOG3562|consensus
Probab=100.00 E-value=8.6e-35 Score=272.44 Aligned_cols=101 Identities=54% Similarity=1.014 Sum_probs=94.8
Q ss_pred CCCCCCCCCHHHHHHHHHhcCCCCCcCHHHHHHHHHhhCCCcccCCCCcccccccccccCcceeeecCCCCCCCCceeeE
Q psy15918 113 KKDEKPPYSYNALIMMAIRQSPEKRLTLNGIYEYIMTNFPYYKTNKQGWQNSIRHNLSLNKCFVKVPRHYDDPGKGNYWM 192 (376)
Q Consensus 113 k~~~KPPySYaaLIa~AI~sSp~krLTL~EIY~wI~~~fPYyr~~~~GWqNSIRHNLSLNkcFvKvpR~~~epGKG~~W~ 192 (376)
-.++||||||+.|.+|||.++++|+|.|.|||+||+++|||||.++..||||+|||||+|+||+||+|..+.+|||+||+
T Consensus 9 Y~dQKPPYSYIsLTaMAI~~SpekmLPLseIYkfImDrFPfYRkNTQrWQNSLRHNLSFNDCFIKiPRr~drpGKGsyWa 88 (277)
T KOG3562|consen 9 YGDQKPPYSYISLTAMAIQSSPEKMLPLSEIYKFIMDRFPFYRKNTQRWQNSLRHNLSFNDCFIKIPRRPDRPGKGSYWA 88 (277)
T ss_pred ccccCCCceeeehhhHHhhcChhhcCcHHHHHHHHHhhCchhhhchHHHHHHhhccccccceeeecCCCCCCCCCcccee
Confidence 35799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCchhhhcCCccCccCCCC
Q psy15918 193 LDASSEDVFIGGTTGKLRRRT 213 (376)
Q Consensus 193 ldP~~e~~f~~G~~~K~RRR~ 213 (376)
|.|.+.++|++|..-++|+|-
T Consensus 89 lHP~a~dMFENGS~LRRrKRF 109 (277)
T KOG3562|consen 89 LHPSAFDMFENGSLLRRRKRF 109 (277)
T ss_pred eccchhhhcccchHHHHhhhh
Confidence 999999999999874444433
No 6
>KOG2294|consensus
Probab=100.00 E-value=2.2e-35 Score=291.34 Aligned_cols=100 Identities=62% Similarity=1.110 Sum_probs=93.9
Q ss_pred CCCCCCCCCHHHHHHHHHhcCCCCCcCHHHHHHHHHh-hCCCcccCC-CCcccccccccccCcceeeecCCCCCCCCcee
Q psy15918 113 KKDEKPPYSYNALIMMAIRQSPEKRLTLNGIYEYIMT-NFPYYKTNK-QGWQNSIRHNLSLNKCFVKVPRHYDDPGKGNY 190 (376)
Q Consensus 113 k~~~KPPySYaaLIa~AI~sSp~krLTL~EIY~wI~~-~fPYyr~~~-~GWqNSIRHNLSLNkcFvKvpR~~~epGKG~~ 190 (376)
+...||||||++||+|||+.+++|||||+|||+||+. +|||||++. .|||||||||||||+||+||+|..+++|||+|
T Consensus 126 ~~~~kpp~SY~~LI~mAI~~Sp~krLtLs~Iy~~i~~~~fpyyr~~~~~gWqNSIRHNLSLn~cF~Kvpr~~~~~gKg~~ 205 (454)
T KOG2294|consen 126 GAGVKPPYSYSGLIAMAIRLSPGKRLTLGGIYFYILLEHFPYYRDANMPGWKNSIRHNLSLNKCFVKVPRERGRPGKGNY 205 (454)
T ss_pred CCCcCCccccccccccccccCCCcceeecCeeEEEEeccccccccCCCccchhhcccccccccCccccCCcccCCCCCCc
Confidence 5679999999999999999999999999999999995 999999999 99999999999999999999999888999999
Q ss_pred eEecCCchh-hhcCCccCccCCC
Q psy15918 191 WMLDASSED-VFIGGTTGKLRRR 212 (376)
Q Consensus 191 W~ldP~~e~-~f~~G~~~K~RRR 212 (376)
|+|||++++ +|++|.+.|+||+
T Consensus 206 W~ldP~~~~~~~~~g~~~rr~~~ 228 (454)
T KOG2294|consen 206 WTLDPDDENNMFDNGSFRRRRRS 228 (454)
T ss_pred cccCcchhccccccccccccccc
Confidence 999999999 8888777666654
No 7
>KOG4385|consensus
Probab=99.87 E-value=3.6e-23 Score=210.24 Aligned_cols=83 Identities=45% Similarity=0.871 Sum_probs=77.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHhcCCCCCcCHHHHHHHHHhhCCCcccCCCCcccccccccccCcceeeecCCCCCCCCcee
Q psy15918 111 ECKKDEKPPYSYNALIMMAIRQSPEKRLTLNGIYEYIMTNFPYYKTNKQGWQNSIRHNLSLNKCFVKVPRHYDDPGKGNY 190 (376)
Q Consensus 111 ~~k~~~KPPySYaaLIa~AI~sSp~krLTL~EIY~wI~~~fPYyr~~~~GWqNSIRHNLSLNkcFvKvpR~~~epGKG~~ 190 (376)
-+..+.||||+|+.||..||+++++|.|||+|||.|+.+.|.|||.+...|||+|||||||++||++|+. -||.-
T Consensus 362 yk~~dvRPPfTYAsLIRqAIlESpdkQLTLNEIY~WFTrtFAYFRRNaATWKnAVRHNLSLHKCF~RVEn-----vkgav 436 (581)
T KOG4385|consen 362 YKNADVRPPFTYASLIRQAILESPDKQLTLNEIYNWFTRTFAYFRRNAATWKNAVRHNLSLHKCFVRVEN-----VKGAV 436 (581)
T ss_pred hhccccCCchhHHHHHHHHHhcCchhhccHHHHHHHHHHHHHHHhccchhHhHHHhhhhHHHHHHHHHHH-----Hhcce
Confidence 3457899999999999999999999999999999999999999999999999999999999999999955 69999
Q ss_pred eEecCCch
Q psy15918 191 WMLDASSE 198 (376)
Q Consensus 191 W~ldP~~e 198 (376)
|++|+...
T Consensus 437 wtvDe~e~ 444 (581)
T KOG4385|consen 437 WTVDEREF 444 (581)
T ss_pred eeeehhhh
Confidence 99997643
No 8
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.83 E-value=3.4e-21 Score=201.96 Aligned_cols=97 Identities=44% Similarity=0.764 Sum_probs=91.3
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHhcCCCCCcCHHHHHHHHHhhCCCcccCCCCcccccccccccCcceeeecCCCCCCC
Q psy15918 107 GKPKECKKDEKPPYSYNALIMMAIRQSPEKRLTLNGIYEYIMTNFPYYKTNKQGWQNSIRHNLSLNKCFVKVPRHYDDPG 186 (376)
Q Consensus 107 ~~~~~~k~~~KPPySYaaLIa~AI~sSp~krLTL~EIY~wI~~~fPYyr~~~~GWqNSIRHNLSLNkcFvKvpR~~~epG 186 (376)
......+...||+++|+.||+.||+.++.++|+|.+||.||..+|||||.+..+|+||||||||||+||.||+|...++|
T Consensus 327 ~~s~~~~~~~kP~~sya~~iT~ail~s~~~kmsls~Iy~~i~s~~pyYr~~p~~w~nSiRhnlSlNksf~kvP~sa~~pG 406 (610)
T COG5025 327 DLSADVNRTSKPAFSYANSITQAILSSPSGKMTLSEIYSWISSNLPYYRHKPTAWQNSIRHNLSLNKSFEKVPRSASQPG 406 (610)
T ss_pred ccccccccCccCCcchhhhhHHHhhcCcccccccccccccccccchhhccCCcccCchhhhhhhhccccccCCCCcCCCC
Confidence 34455678999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceeeEecCCchhhhcC
Q psy15918 187 KGNYWMLDASSEDVFIG 203 (376)
Q Consensus 187 KG~~W~ldP~~e~~f~~ 203 (376)
||+||+||.++...|..
T Consensus 407 Kg~fw~i~~s~~~~~~s 423 (610)
T COG5025 407 KGCFWKIDYSYIYEKES 423 (610)
T ss_pred CcccCccChhhhhhhcc
Confidence 99999999999888754
No 9
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.50 E-value=2.6e-15 Score=158.07 Aligned_cols=91 Identities=42% Similarity=0.689 Sum_probs=86.5
Q ss_pred CCCCCCCCCHHHHHHHHHhcCCCCCcCHHHHHHHHHhhCCCcccCCCCcccccccccccCcceeeecCCCCCCCCceeeE
Q psy15918 113 KKDEKPPYSYNALIMMAIRQSPEKRLTLNGIYEYIMTNFPYYKTNKQGWQNSIRHNLSLNKCFVKVPRHYDDPGKGNYWM 192 (376)
Q Consensus 113 k~~~KPPySYaaLIa~AI~sSp~krLTL~EIY~wI~~~fPYyr~~~~GWqNSIRHNLSLNkcFvKvpR~~~epGKG~~W~ 192 (376)
.-..||||+|+.||.++|.++++++|||..||.||-..|.||.....+|+|+|||||++|++|.|+.+..+-.+||.||.
T Consensus 82 ~t~~v~~~s~a~gr~~~il~s~~~~lt~s~~~~~~~~~~~~~~k~~~~~~~sIr~Nls~~~a~~~i~g~~g~~~~g~~~~ 161 (610)
T COG5025 82 WTYYVPPYSYATGRGLAILNSPDKPLTLSKIYTWIHNTFFYYAKVVSRWQNSIRHNLSLNDAFIKIEGRNGAKVKGHFWS 161 (610)
T ss_pred cccccCCeeeeeccccccccCcccCCcccceeeeeeecccccccccchhhhhhhcccccCceEEEEeccCCccccceeec
Confidence 34589999999999999999999999999999999999999999999999999999999999999999998899999999
Q ss_pred ecCCchhhhcC
Q psy15918 193 LDASSEDVFIG 203 (376)
Q Consensus 193 ldP~~e~~f~~ 203 (376)
|.|+.+..|..
T Consensus 162 igP~~~~~~l~ 172 (610)
T COG5025 162 IGPGHETQFLK 172 (610)
T ss_pred cCCCccceeec
Confidence 99999888764
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=92.97 E-value=0.14 Score=40.67 Aligned_cols=33 Identities=30% Similarity=0.519 Sum_probs=29.2
Q ss_pred CHHHHHHHHHhcCCC-CCcCHHHHHHHHHhhCCC
Q psy15918 121 SYNALIMMAIRQSPE-KRLTLNGIYEYIMTNFPY 153 (376)
Q Consensus 121 SYaaLIa~AI~sSp~-krLTL~EIY~wI~~~fPY 153 (376)
+|..||..||.+..+ +..++..|..||+++|+.
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 599999999998655 679999999999999864
No 11
>smart00526 H15 Domain in histone families 1 and 5.
Probab=92.06 E-value=0.15 Score=39.16 Aligned_cols=32 Identities=34% Similarity=0.509 Sum_probs=28.4
Q ss_pred CHHHHHHHHHhcCCC-CCcCHHHHHHHHHhhCC
Q psy15918 121 SYNALIMMAIRQSPE-KRLTLNGIYEYIMTNFP 152 (376)
Q Consensus 121 SYaaLIa~AI~sSp~-krLTL~EIY~wI~~~fP 152 (376)
+|..||..||....+ +..++..|..||+.+|.
T Consensus 6 ~~~~mI~eAI~~l~er~GsS~~aI~kyi~~~~~ 38 (66)
T smart00526 6 PYSEMITEAISALKERKGSSLQAIKKYIEANYK 38 (66)
T ss_pred CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCC
Confidence 799999999998665 55999999999999965
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=88.91 E-value=0.65 Score=37.95 Aligned_cols=55 Identities=20% Similarity=0.357 Sum_probs=37.9
Q ss_pred CHHHHHHHHHhcC-CCCCcCHHHHHHHHHhhCCCcccCCCCccccccccc---ccCcceeee
Q psy15918 121 SYNALIMMAIRQS-PEKRLTLNGIYEYIMTNFPYYKTNKQGWQNSIRHNL---SLNKCFVKV 178 (376)
Q Consensus 121 SYaaLIa~AI~sS-p~krLTL~EIY~wI~~~fPYyr~~~~GWqNSIRHNL---SLNkcFvKv 178 (376)
+|..||..||... ..+..++..|..||+.+|+.-. ..+..-++..| -.+..|+++
T Consensus 6 ~y~~MI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~---~~~~~~l~~aLkk~v~~G~l~~~ 64 (88)
T cd00073 6 PYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDD---ENFNKLLKLALKKGVAKGKLVQV 64 (88)
T ss_pred CHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCcch---HHHHHHHHHHHHHHHHCCCeEee
Confidence 7999999999984 4566999999999999987432 23333343333 224566655
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=88.27 E-value=0.4 Score=37.27 Aligned_cols=57 Identities=21% Similarity=0.295 Sum_probs=37.7
Q ss_pred CCHHHHHHHHHhcCCCCCcCHHHHHHHHHhhCCCcccCCCCcccccccccc-----cCcceeee
Q psy15918 120 YSYNALIMMAIRQSPEKRLTLNGIYEYIMTNFPYYKTNKQGWQNSIRHNLS-----LNKCFVKV 178 (376)
Q Consensus 120 ySYaaLIa~AI~sSp~krLTL~EIY~wI~~~fPYyr~~~~GWqNSIRHNLS-----LNkcFvKv 178 (376)
+||..++...|+... +-|+++||++.|.+.-- |....+...++|+-.|. .+..|++|
T Consensus 1 mt~~eaa~~vL~~~~-~pm~~~eI~~~i~~~~~-~~~~~k~p~~~i~a~ly~~~~~~d~~F~~v 62 (72)
T PF05066_consen 1 MTFKEAAYEVLEEAG-RPMTFKEIWEEIQERGL-YKKSGKTPEATIAAQLYTDIKNEDSRFVKV 62 (72)
T ss_dssp S-HHHHHHHHHHHH--S-EEHHHHHHHHHHHHT-S---GGGGGHHHH-HHHHHHH-T-SS-EES
T ss_pred CCHHHHHHHHHHhcC-CCcCHHHHHHHHHHhCC-CCcccCCHHHHHHHHHHHHcccCCCCEEEe
Confidence 478888888888887 66999999999998744 33336677788873333 45689998
No 14
>KOG4012|consensus
Probab=69.34 E-value=4.5 Score=39.68 Aligned_cols=66 Identities=30% Similarity=0.425 Sum_probs=44.8
Q ss_pred CCCHHHHHHHHHhcCCC-CCcCHHHHHHHHHhhCCCcccCCCCcccccccccccC-----cceeeecCCCCCCCCceeeE
Q psy15918 119 PYSYNALIMMAIRQSPE-KRLTLNGIYEYIMTNFPYYKTNKQGWQNSIRHNLSLN-----KCFVKVPRHYDDPGKGNYWM 192 (376)
Q Consensus 119 PySYaaLIa~AI~sSp~-krLTL~EIY~wI~~~fPYyr~~~~GWqNSIRHNLSLN-----kcFvKvpR~~~epGKG~~W~ 192 (376)
.-+|+.||..||...-+ ...++.-|+.||.++|+.|.-.. |.-|.+++|+ ..|+++ + |.|.-|.
T Consensus 44 ~P~~~~mi~eAi~a~keR~GsS~aAikK~i~~~Y~g~~v~k----~n~~lk~alK~~v~~g~l~Qt-k-----G~GAsGs 113 (243)
T KOG4012|consen 44 HPPYSEMITEAISALKERKGSSLAAIKKYIAANYPGDDVEK----NNSRLKLALKKGVSKGVLVQT-K-----GTGASGS 113 (243)
T ss_pred CCcHHHHHHHHHHHhhhcccchHHHHHHHHhhcCccchhhh----hhHHHHHHHHhhhccCceeee-c-----cCCcccc
Confidence 33599999999998654 45999999999999998665322 2345555554 345443 1 5665555
Q ss_pred ec
Q psy15918 193 LD 194 (376)
Q Consensus 193 ld 194 (376)
+.
T Consensus 114 Fk 115 (243)
T KOG4012|consen 114 FK 115 (243)
T ss_pred cc
Confidence 44
No 15
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=66.13 E-value=4.4 Score=32.99 Aligned_cols=73 Identities=21% Similarity=0.349 Sum_probs=46.6
Q ss_pred CHHHHHHHHHhcCC--CCCcCHHHHHHHHHhhCCCcc--------cCC--CCcccccccccccCcceeeecCCCCCCCCc
Q psy15918 121 SYNALIMMAIRQSP--EKRLTLNGIYEYIMTNFPYYK--------TNK--QGWQNSIRHNLSLNKCFVKVPRHYDDPGKG 188 (376)
Q Consensus 121 SYaaLIa~AI~sSp--~krLTL~EIY~wI~~~fPYyr--------~~~--~GWqNSIRHNLSLNkcFvKvpR~~~epGKG 188 (376)
+|..|+...|+.-. ++.++.+||++.|.++|..=. ... .-|+|.|+=.++--++.--|.+ +++|
T Consensus 1 ~~~~~~~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~~~~~~~sg~~~~~~~~ri~Wa~~~L~~aGli~~----~~rG 76 (92)
T PF14338_consen 1 TYDELMPPILEALKDLGGSASRKEIYERVAERFGLSDEERNERLPSGQGYSRFKNRIRWARSYLKKAGLIER----PKRG 76 (92)
T ss_pred CHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHhCCCHHHHHHHcccCCcchhHHHhHHHHHHHHHHCCCccC----CCCC
Confidence 35566665555422 466999999999999987321 111 2599999876665444433322 2445
Q ss_pred eeeEecCCch
Q psy15918 189 NYWMLDASSE 198 (376)
Q Consensus 189 ~~W~ldP~~e 198 (376)
.|.|.+.-.
T Consensus 77 -~~~iT~~G~ 85 (92)
T PF14338_consen 77 -IWRITEKGR 85 (92)
T ss_pred -ceEECHhHH
Confidence 999997643
No 16
>KOG1924|consensus
Probab=58.11 E-value=38 Score=38.87 Aligned_cols=8 Identities=38% Similarity=0.439 Sum_probs=3.2
Q ss_pred HHHHHHHH
Q psy15918 122 YNALIMMA 129 (376)
Q Consensus 122 YaaLIa~A 129 (376)
|..||..+
T Consensus 424 YykLIEec 431 (1102)
T KOG1924|consen 424 YYKLIEEC 431 (1102)
T ss_pred HHHHHHHH
Confidence 33444433
No 17
>KOG1528|consensus
Probab=43.76 E-value=8.5 Score=39.32 Aligned_cols=38 Identities=34% Similarity=0.543 Sum_probs=26.8
Q ss_pred cccccCcceeeecCCCCCC-CCceeeEecCCchhhhcCCccCccC
Q psy15918 167 HNLSLNKCFVKVPRHYDDP-GKGNYWMLDASSEDVFIGGTTGKLR 210 (376)
Q Consensus 167 HNLSLNkcFvKvpR~~~ep-GKG~~W~ldP~~e~~f~~G~~~K~R 210 (376)
.-||+.+...-+.|...+. .||.+|.|||- .|+.|-+|
T Consensus 109 ~~ls~~dvl~aID~G~s~GG~kGrhWvLDPI------DGTrGFlR 147 (351)
T KOG1528|consen 109 SPLSSDDVLKAIDRGNSEGGPKGRHWVLDPI------DGTRGFLR 147 (351)
T ss_pred CCCCHHHHHHHHhcccccCCCCCceEEeccC------CCcccccc
Confidence 4577777777777776444 48999999994 55555544
No 18
>COG2958 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.28 E-value=30 Score=34.90 Aligned_cols=71 Identities=21% Similarity=0.343 Sum_probs=48.1
Q ss_pred CHHHHHHHHHhcCCCCCcCHHHHHHHHHhhCCC------cccCCCC------cccccccccccCcceeeecCCCCCCCCc
Q psy15918 121 SYNALIMMAIRQSPEKRLTLNGIYEYIMTNFPY------YKTNKQG------WQNSIRHNLSLNKCFVKVPRHYDDPGKG 188 (376)
Q Consensus 121 SYaaLIa~AI~sSp~krLTL~EIY~wI~~~fPY------yr~~~~G------WqNSIRHNLSLNkcFvKvpR~~~epGKG 188 (376)
+|..+|-..|+. .+..+|..|||+|+.+.||- |...+.. =.-+.|-||-.+--|.||.- |..
T Consensus 6 ~~~e~vl~~Lq~-~~ep~t~~eI~eka~e~~~~~~~~kk~~s~g~tp~q~va~~iy~~~~lq~~~pflKvte-----~P~ 79 (307)
T COG2958 6 NLIEIVLSVLQT-SEEPFTAREIAEKAFETFPAECQEKKFDSGGDTPQQLVAEIIYTRPNLQEKHPFLKVTE-----GPR 79 (307)
T ss_pred hhHHHHHHHHHc-cCCCCcHHHHHHHHHHhccHHHHHHhhccccccHHHHHHHHHhcCccccccCccccccc-----Cce
Confidence 466666666666 67779999999999999982 2222221 23367889999999999833 456
Q ss_pred eeeEecCCc
Q psy15918 189 NYWMLDASS 197 (376)
Q Consensus 189 ~~W~ldP~~ 197 (376)
-||--+-+.
T Consensus 80 ~~~lke~~~ 88 (307)
T COG2958 80 LYYLKEAAD 88 (307)
T ss_pred EEeeccccc
Confidence 677544433
No 19
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=37.02 E-value=37 Score=25.77 Aligned_cols=54 Identities=15% Similarity=0.254 Sum_probs=35.9
Q ss_pred HHHHHHHHHhcCCC--CCcCHHHHHHHHHhhCCCcccCCCCccccccccc-ccCccee
Q psy15918 122 YNALIMMAIRQSPE--KRLTLNGIYEYIMTNFPYYKTNKQGWQNSIRHNL-SLNKCFV 176 (376)
Q Consensus 122 YaaLIa~AI~sSp~--krLTL~EIY~wI~~~fPYyr~~~~GWqNSIRHNL-SLNkcFv 176 (376)
-..+|..+|.+..+ +.+.|++|..++.++||-|....=|.. ++++-| ++-+.|+
T Consensus 6 ~~~~l~~ll~~~~~~~g~v~ls~l~~~~~~~~~~f~~~~yG~~-~l~~ll~~~~~~~~ 62 (74)
T PF12872_consen 6 LKKLLRELLESQKGEDGWVSLSQLGQEYKKKYPDFDPRDYGFS-SLSELLESLPDVVE 62 (74)
T ss_dssp HHHHHHHHHHHTCTTTSSEEHHHHHHHHHHHHTT--TCCTTSS-SHHHHHHT-TTTEE
T ss_pred HHHHHHHHHHhCcCCCceEEHHHHHHHHHHHCCCCCccccCCC-cHHHHHHhCCCeEE
Confidence 35678888855443 479999999999999988876655543 455555 5556554
No 20
>cd06649 PKc_MEK2 Catalytic domain of the dual-specificity Protein Kinase, MAP/ERK Kinase 2. Protein kinases (PKs), MAP/ERK Kinase (MEK) 2 subfamily, catalytic (c) domain. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine or tyrosine residues on protein substrates. The MEK subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. The mitogen-activated protein (MAP) kinase signaling pathways are important mediators of cellular responses to extracellular signals. The pathways involve a triple kinase core cascade comprising the MAP kinase (MAPK), which is phosphorylated and activated by a MAPK kinase (MAPKK or MKK), which itself is phosphorylated and activated by a MAPK kinase kinase (MAPKKK or MKKK). MEK2 is a dual-specificity PK that phosphorylates and activates the downst
Probab=24.67 E-value=43 Score=31.92 Aligned_cols=49 Identities=14% Similarity=0.309 Sum_probs=39.8
Q ss_pred HHHHHHHHHhcCCCCCcCHHHHHHHHHhhCCCccc---CCCCcccccccccccCcce
Q psy15918 122 YNALIMMAIRQSPEKRLTLNGIYEYIMTNFPYYKT---NKQGWQNSIRHNLSLNKCF 175 (376)
Q Consensus 122 YaaLIa~AI~sSp~krLTL~EIY~wI~~~fPYyr~---~~~GWqNSIRHNLSLNkcF 175 (376)
+..||...+.-.|++|.|..||.+ .|||+. ....|++.+.-+|+++.-+
T Consensus 277 l~~li~~~L~~~P~~Rpt~~ell~-----h~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 (331)
T cd06649 277 FQEFVNKCLIKNPAERADLKMLMN-----HTFIKRSEVEEVDFAGWLCKTLRLNQPS 328 (331)
T ss_pred HHHHHHHHccCCcccCCCHHHHhc-----ChHHhhcccccccHHHHHHHhhcccccc
Confidence 689999999999999999999974 466764 3567899998888887543
Done!