Query psy6883
Match_columns 414
No_of_seqs 245 out of 866
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 20:56:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6883.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6883hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3563|consensus 100.0 7.1E-40 1.5E-44 325.6 12.2 110 139-248 167-276 (454)
2 KOG3562|consensus 100.0 1.8E-39 4E-44 306.9 9.3 105 141-245 9-113 (277)
3 PF00250 Fork_head: Fork head 100.0 4.3E-38 9.4E-43 262.9 2.2 96 145-240 1-96 (96)
4 cd00059 FH Forkhead (FH), also 100.0 7.2E-37 1.6E-41 247.9 7.2 78 145-222 1-78 (78)
5 smart00339 FH FORKHEAD. FORKHE 100.0 7.5E-36 1.6E-40 246.7 7.1 87 145-231 1-87 (89)
6 KOG2294|consensus 100.0 2.8E-36 6E-41 299.2 -0.7 104 141-244 126-232 (454)
7 KOG4385|consensus 99.8 2.4E-22 5.3E-27 206.2 0.6 81 139-224 362-442 (581)
8 COG5025 Transcription factor o 99.8 5.8E-21 1.2E-25 202.0 5.1 100 134-233 326-425 (610)
9 COG5025 Transcription factor o 99.5 1.3E-15 2.9E-20 161.6 -0.7 92 142-233 83-174 (610)
10 PF00538 Linker_histone: linke 91.6 0.22 4.9E-06 39.9 3.6 33 149-181 4-37 (77)
11 smart00526 H15 Domain in histo 90.8 0.33 7.2E-06 37.7 3.7 32 149-180 6-38 (66)
12 cd00073 H15 linker histone 1 a 87.7 0.81 1.7E-05 37.8 4.1 34 149-182 6-40 (88)
13 PF05066 HARE-HTH: HB1, ASXL, 79.4 1.5 3.2E-05 34.5 2.2 58 148-207 1-63 (72)
14 KOG1924|consensus 77.9 8.1 0.00018 44.4 8.0 10 150-159 424-433 (1102)
15 KOG1924|consensus 67.6 11 0.00025 43.2 6.2 17 36-52 322-338 (1102)
16 KOG4012|consensus 62.0 8.1 0.00017 38.4 3.4 52 146-201 43-95 (243)
17 PF14338 Mrr_N: Mrr N-terminal 57.8 8.1 0.00018 31.8 2.2 71 149-224 1-83 (92)
18 PF12872 OST-HTH: OST-HTH/LOTU 44.9 16 0.00034 28.2 1.9 53 150-203 6-61 (74)
19 COG2958 Uncharacterized protei 43.7 27 0.00059 35.6 3.8 69 149-223 6-86 (307)
20 KOG2236|consensus 22.2 2.6E+02 0.0056 30.7 6.9 17 28-44 84-100 (483)
No 1
>KOG3563|consensus
Probab=100.00 E-value=7.1e-40 Score=325.57 Aligned_cols=110 Identities=57% Similarity=1.045 Sum_probs=105.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCCccCCCccccccccccccccccccccCCCCCCCCcee
Q psy6883 139 GKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNY 218 (414)
Q Consensus 139 ~~~~~~KPPySYaaLIa~AI~sSP~kkLTLsEIYewI~~~FPYYr~~~~GWQNSIRHNLSLNkcFvKVpR~~~~pGKGsy 218 (414)
..-...||||||+.||+|||+.+|.|+|||+|||+||++.|||||.+...|||||||.||+|+||+||+|.++.||||+|
T Consensus 167 RsY~haKPPYSYISLITMAIQ~~pskmLTLSEIYqwIMDLFPyYrqNQQRWQNSIRHSLSFNDCFVKVaRSPDKPGKGSf 246 (454)
T KOG3563|consen 167 RSYTHAKPPYSYISLITMAIQQAPSKMLTLSEIYQWIMDLFPYYRQNQQRWQNSIRHSLSFNDCFVKVARSPDKPGKGSF 246 (454)
T ss_pred ccccCCCCChhHHHHHHHHHHhCCccceeHHHHHHHHHHhhhHhhhhHHHHHhhhhhhccccceeeeccCCCCCCCCccc
Confidence 34567999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecCcchhcccCCceeecccccCCCCCCc
Q psy6883 219 WTLDPMAEDMFDNGSFLRRRKRYKRTPPDF 248 (414)
Q Consensus 219 WtLdP~ae~~f~~Gs~lRRRKR~kr~~p~~ 248 (414)
|+|+|.+.+||+||.++||+||||..+++.
T Consensus 247 WTLHpdsGNMFENGCYLRRQKRFK~ekk~~ 276 (454)
T KOG3563|consen 247 WTLHPDSGNMFENGCYLRRQKRFKCEKKEA 276 (454)
T ss_pred eeecCCcCcccccchhehhhhhhhhhhhhc
Confidence 999999999999999999999999877655
No 2
>KOG3562|consensus
Probab=100.00 E-value=1.8e-39 Score=306.92 Aligned_cols=105 Identities=62% Similarity=1.117 Sum_probs=102.1
Q ss_pred CCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCCccCCCccccccccccccccccccccCCCCCCCCceeEE
Q psy6883 141 NSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWT 220 (414)
Q Consensus 141 ~~~~KPPySYaaLIa~AI~sSP~kkLTLsEIYewI~~~FPYYr~~~~GWQNSIRHNLSLNkcFvKVpR~~~~pGKGsyWt 220 (414)
-..+||||||+.|.+|||.++|+|+|.|+|||+||+++|||||.+++.||||+|||||+|+||+||+|..+.+|||+||+
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 ecCcchhcccCCceeecccccCCCC
Q psy6883 221 LDPMAEDMFDNGSFLRRRKRYKRTP 245 (414)
Q Consensus 221 LdP~ae~~f~~Gs~lRRRKR~kr~~ 245 (414)
|+|.+.+||+||+++|||||+|-.+
T Consensus 89 lHP~a~dMFENGS~LRRrKRFrv~k 113 (277)
T KOG3562|consen 89 LHPSAFDMFENGSLLRRRKRFRVLK 113 (277)
T ss_pred eccchhhhcccchHHHHhhhhhhcc
Confidence 9999999999999999999999765
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=4.3e-38 Score=262.91 Aligned_cols=96 Identities=66% Similarity=1.208 Sum_probs=89.9
Q ss_pred CCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCCccCCCccccccccccccccccccccCCCCCCCCceeEEecCc
Q psy6883 145 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPM 224 (414)
Q Consensus 145 KPPySYaaLIa~AI~sSP~kkLTLsEIYewI~~~FPYYr~~~~GWQNSIRHNLSLNkcFvKVpR~~~~pGKGsyWtLdP~ 224 (414)
||||||++||+|||+++|+++|||+|||+||+++||||+.+..+||||||||||+|+||+||++..+.+|||+||+|+++
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 89999999999999999999999999999999999999999999999999999999999999998788899999999999
Q ss_pred chhcccCCceeecccc
Q psy6883 225 AEDMFDNGSFLRRRKR 240 (414)
Q Consensus 225 ae~~f~~Gs~lRRRKR 240 (414)
+...|+++.++|||||
T Consensus 81 ~~~~~~~~~~~~~~~~ 96 (96)
T PF00250_consen 81 AIEEFEKGRFKRRRKR 96 (96)
T ss_dssp HHHHHHHSCCSSSSSS
T ss_pred HHHHHhcchhhhhhcc
Confidence 9999999999888875
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=7.2e-37 Score=247.86 Aligned_cols=78 Identities=69% Similarity=1.249 Sum_probs=76.7
Q ss_pred CCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCCccCCCccccccccccccccccccccCCCCCCCCceeEEec
Q psy6883 145 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLD 222 (414)
Q Consensus 145 KPPySYaaLIa~AI~sSP~kkLTLsEIYewI~~~FPYYr~~~~GWQNSIRHNLSLNkcFvKVpR~~~~pGKGsyWtLd 222 (414)
||||||++||++||+++|+++|||+|||+||+++|||||.+..|||||||||||+|+||+||+|..+.+|||+||+||
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 5
>smart00339 FH FORKHEAD. FORKHEAD, also known as a "winged helix"
Probab=100.00 E-value=7.5e-36 Score=246.66 Aligned_cols=87 Identities=74% Similarity=1.277 Sum_probs=83.0
Q ss_pred CCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCCccCCCccccccccccccccccccccCCCCCCCCceeEEecCc
Q psy6883 145 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPM 224 (414)
Q Consensus 145 KPPySYaaLIa~AI~sSP~kkLTLsEIYewI~~~FPYYr~~~~GWQNSIRHNLSLNkcFvKVpR~~~~pGKGsyWtLdP~ 224 (414)
||||||++||++||+++|+++|||+|||+||+++|||||.+..|||||||||||+|+||+||+|..+.+|||+||+|+|+
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 chhcccC
Q psy6883 225 AEDMFDN 231 (414)
Q Consensus 225 ae~~f~~ 231 (414)
++.+|..
T Consensus 81 ~~~~~~~ 87 (89)
T smart00339 81 AENMFEN 87 (89)
T ss_pred HHHHHhc
Confidence 9875553
No 6
>KOG2294|consensus
Probab=100.00 E-value=2.8e-36 Score=299.24 Aligned_cols=104 Identities=65% Similarity=1.146 Sum_probs=98.2
Q ss_pred CCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHh-cCCCCccCC-CccccccccccccccccccccCCCCCCCCcee
Q psy6883 141 NSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMS-RFPYYREKF-PAWQNSIRHNLSLNDCFVKIPREPGNPGKGNY 218 (414)
Q Consensus 141 ~~~~KPPySYaaLIa~AI~sSP~kkLTLsEIYewI~~-~FPYYr~~~-~GWQNSIRHNLSLNkcFvKVpR~~~~pGKGsy 218 (414)
...+||||||++||+|||+.+++|+|||+|||+||+. +|||||++. .|||||||||||||+||+||+|+.+.+|||+|
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 4579999999999999999999999999999999995 999999999 99999999999999999999999889999999
Q ss_pred EEecCcchh-cccCCceeecccccCCC
Q psy6883 219 WTLDPMAED-MFDNGSFLRRRKRYKRT 244 (414)
Q Consensus 219 WtLdP~ae~-~f~~Gs~lRRRKR~kr~ 244 (414)
|+|||..++ ||++|.|+|||+++++.
T Consensus 206 W~ldP~~~~~~~~~g~~~rr~~~~~~~ 232 (454)
T KOG2294|consen 206 WTLDPDDENNMFDNGSFRRRRRSKSNG 232 (454)
T ss_pred cccCcchhccccccccccccccccccc
Confidence 999999999 99999999888875544
No 7
>KOG4385|consensus
Probab=99.84 E-value=2.4e-22 Score=206.15 Aligned_cols=81 Identities=46% Similarity=0.899 Sum_probs=76.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCCccCCCccccccccccccccccccccCCCCCCCCcee
Q psy6883 139 GKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNY 218 (414)
Q Consensus 139 ~~~~~~KPPySYaaLIa~AI~sSP~kkLTLsEIYewI~~~FPYYr~~~~GWQNSIRHNLSLNkcFvKVpR~~~~pGKGsy 218 (414)
.++-.++|||+|+.||..||+.+|++.|||+|||.|+.+.|.|||.+...|||+|||||||+|||++|+.- ||--
T Consensus 362 yk~~dvRPPfTYAsLIRqAIlESpdkQLTLNEIY~WFTrtFAYFRRNaATWKnAVRHNLSLHKCF~RVEnv-----kgav 436 (581)
T KOG4385|consen 362 YKNADVRPPFTYASLIRQAILESPDKQLTLNEIYNWFTRTFAYFRRNAATWKNAVRHNLSLHKCFVRVENV-----KGAV 436 (581)
T ss_pred hhccccCCchhHHHHHHHHHhcCchhhccHHHHHHHHHHHHHHHhccchhHhHHHhhhhHHHHHHHHHHHH-----hcce
Confidence 45778999999999999999999999999999999999999999999999999999999999999999874 8999
Q ss_pred EEecCc
Q psy6883 219 WTLDPM 224 (414)
Q Consensus 219 WtLdP~ 224 (414)
|++|..
T Consensus 437 wtvDe~ 442 (581)
T KOG4385|consen 437 WTVDER 442 (581)
T ss_pred eeeehh
Confidence 999964
No 8
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.82 E-value=5.8e-21 Score=201.95 Aligned_cols=100 Identities=49% Similarity=0.755 Sum_probs=92.0
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCCccCCCccccccccccccccccccccCCCCCC
Q psy6883 134 SDKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNP 213 (414)
Q Consensus 134 ~~~~~~~~~~~KPPySYaaLIa~AI~sSP~kkLTLsEIYewI~~~FPYYr~~~~GWQNSIRHNLSLNkcFvKVpR~~~~p 213 (414)
+.+....+...||+++|+.||+.||+.++.++|+|.+||.||..+|||||.+..+||||||||||+|++|.||+|....+
T Consensus 326 s~~s~~~~~~~kP~~sya~~iT~ail~s~~~kmsls~Iy~~i~s~~pyYr~~p~~w~nSiRhnlSlNksf~kvP~sa~~p 405 (610)
T COG5025 326 SDLSADVNRTSKPAFSYANSITQAILSSPSGKMTLSEIYSWISSNLPYYRHKPTAWQNSIRHNLSLNKSFEKVPRSASQP 405 (610)
T ss_pred CccccccccCccCCcchhhhhHHHhhcCcccccccccccccccccchhhccCCcccCchhhhhhhhccccccCCCCcCCC
Confidence 44555677899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceeEEecCcchhcccCCc
Q psy6883 214 GKGNYWTLDPMAEDMFDNGS 233 (414)
Q Consensus 214 GKGsyWtLdP~ae~~f~~Gs 233 (414)
|||+||+|+..+...|..-.
T Consensus 406 GKg~fw~i~~s~~~~~~sk~ 425 (610)
T COG5025 406 GKGCFWKIDYSYIYEKESKR 425 (610)
T ss_pred CCcccCccChhhhhhhcccc
Confidence 99999999998876665433
No 9
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.51 E-value=1.3e-15 Score=161.61 Aligned_cols=92 Identities=47% Similarity=0.770 Sum_probs=86.2
Q ss_pred CCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCCccCCCccccccccccccccccccccCCCCCCCCceeEEe
Q psy6883 142 SIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTL 221 (414)
Q Consensus 142 ~~~KPPySYaaLIa~AI~sSP~kkLTLsEIYewI~~~FPYYr~~~~GWQNSIRHNLSLNkcFvKVpR~~~~pGKGsyWtL 221 (414)
-.-||||+|+.+|.++|++++.++|||..||.||...|.||.....+|||+|||||++|++|.||.+..+..+||.||.|
T Consensus 83 t~~v~~~s~a~gr~~~il~s~~~~lt~s~~~~~~~~~~~~~~k~~~~~~~sIr~Nls~~~a~~~i~g~~g~~~~g~~~~i 162 (610)
T COG5025 83 TYYVPPYSYATGRGLAILNSPDKPLTLSKIYTWIHNTFFYYAKVVSRWQNSIRHNLSLNDAFIKIEGRNGAKVKGHFWSI 162 (610)
T ss_pred ccccCCeeeeeccccccccCcccCCcccceeeeeeecccccccccchhhhhhhcccccCceEEEEeccCCccccceeecc
Confidence 34789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCcchhcccCCc
Q psy6883 222 DPMAEDMFDNGS 233 (414)
Q Consensus 222 dP~ae~~f~~Gs 233 (414)
.|..+..|..+.
T Consensus 163 gP~~~~~~l~~g 174 (610)
T COG5025 163 GPGHETQFLKSG 174 (610)
T ss_pred CCCccceeeccc
Confidence 998887765433
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=91.59 E-value=0.22 Score=39.93 Aligned_cols=33 Identities=24% Similarity=0.357 Sum_probs=28.8
Q ss_pred CHHHHHHHHHhcC-CCCCCCHHHHHHHHHhcCCC
Q psy6883 149 SYIALITMAILQS-PHKKLTLSGICEFIMSRFPY 181 (414)
Q Consensus 149 SYaaLIa~AI~sS-P~kkLTLsEIYewI~~~FPY 181 (414)
+|..||.+||.+. ..+..+++.|..||+.+|+.
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 4999999999974 44789999999999999964
No 11
>smart00526 H15 Domain in histone families 1 and 5.
Probab=90.77 E-value=0.33 Score=37.72 Aligned_cols=32 Identities=28% Similarity=0.390 Sum_probs=27.9
Q ss_pred CHHHHHHHHHhcCC-CCCCCHHHHHHHHHhcCC
Q psy6883 149 SYIALITMAILQSP-HKKLTLSGICEFIMSRFP 180 (414)
Q Consensus 149 SYaaLIa~AI~sSP-~kkLTLsEIYewI~~~FP 180 (414)
+|..||..||.... .+..+++.|..||+.+|+
T Consensus 6 ~~~~mI~eAI~~l~er~GsS~~aI~kyi~~~~~ 38 (66)
T smart00526 6 PYSEMITEAISALKERKGSSLQAIKKYIEANYK 38 (66)
T ss_pred CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCC
Confidence 79999999999744 467999999999999965
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=87.67 E-value=0.81 Score=37.85 Aligned_cols=34 Identities=24% Similarity=0.366 Sum_probs=29.4
Q ss_pred CHHHHHHHHHhc-CCCCCCCHHHHHHHHHhcCCCC
Q psy6883 149 SYIALITMAILQ-SPHKKLTLSGICEFIMSRFPYY 182 (414)
Q Consensus 149 SYaaLIa~AI~s-SP~kkLTLsEIYewI~~~FPYY 182 (414)
+|..||.+||.. ...+..+++.|..||+.+|+.-
T Consensus 6 ~y~~MI~eAI~~l~er~GsS~~aI~kyI~~~y~~~ 40 (88)
T cd00073 6 PYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVD 40 (88)
T ss_pred CHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCcc
Confidence 699999999986 5567889999999999998743
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=79.39 E-value=1.5 Score=34.53 Aligned_cols=58 Identities=19% Similarity=0.198 Sum_probs=37.7
Q ss_pred CCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCCccCCCccccccccccc-----ccccccccc
Q psy6883 148 YSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLS-----LNDCFVKIP 207 (414)
Q Consensus 148 ySYaaLIa~AI~sSP~kkLTLsEIYewI~~~FPYYr~~~~GWQNSIRHNLS-----LNkcFvKVp 207 (414)
+||..++...|+... +.|+.+||++.|.++--| ....+...++|+-.|. .+..|++|-
T Consensus 1 mt~~eaa~~vL~~~~-~pm~~~eI~~~i~~~~~~-~~~~k~p~~~i~a~ly~~~~~~d~~F~~vg 63 (72)
T PF05066_consen 1 MTFKEAAYEVLEEAG-RPMTFKEIWEEIQERGLY-KKSGKTPEATIAAQLYTDIKNEDSRFVKVG 63 (72)
T ss_dssp S-HHHHHHHHHHHH--S-EEHHHHHHHHHHHHTS----GGGGGHHHH-HHHHHHH-T-SS-EESS
T ss_pred CCHHHHHHHHHHhcC-CCcCHHHHHHHHHHhCCC-CcccCCHHHHHHHHHHHHcccCCCCEEEeC
Confidence 478888888888876 999999999999976543 3325667778873333 455899873
No 14
>KOG1924|consensus
Probab=77.95 E-value=8.1 Score=44.36 Aligned_cols=10 Identities=40% Similarity=0.501 Sum_probs=8.3
Q ss_pred HHHHHHHHHh
Q psy6883 150 YIALITMAIL 159 (414)
Q Consensus 150 YaaLIa~AI~ 159 (414)
|..||..+|.
T Consensus 424 YykLIEecIS 433 (1102)
T KOG1924|consen 424 YYKLIEECIS 433 (1102)
T ss_pred HHHHHHHHHH
Confidence 8889988874
No 15
>KOG1924|consensus
Probab=67.64 E-value=11 Score=43.23 Aligned_cols=17 Identities=24% Similarity=0.270 Sum_probs=9.7
Q ss_pred cCCCCCCCCccccCCCC
Q psy6883 36 LRGAPHPGDMYLRGAPH 52 (414)
Q Consensus 36 ~~~~~~~~~~~~~g~~h 52 (414)
|--.+|--+|+.|-+-|
T Consensus 322 ldfRlhlR~E~mr~gL~ 338 (1102)
T KOG1924|consen 322 LDFRLHLRSEFMRDGLH 338 (1102)
T ss_pred hhHHHHHHHHHHHHhHH
Confidence 33335666666666655
No 16
>KOG4012|consensus
Probab=62.04 E-value=8.1 Score=38.42 Aligned_cols=52 Identities=27% Similarity=0.351 Sum_probs=38.1
Q ss_pred CCCCHHHHHHHHHhcC-CCCCCCHHHHHHHHHhcCCCCccCCCcccccccccccccc
Q psy6883 146 PPYSYIALITMAILQS-PHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLND 201 (414)
Q Consensus 146 PPySYaaLIa~AI~sS-P~kkLTLsEIYewI~~~FPYYr~~~~GWQNSIRHNLSLNk 201 (414)
+.-+|+.||..||... ......+.-|+.||..+|+.|.-. +|--|.+++|+.
T Consensus 43 ~~P~~~~mi~eAi~a~keR~GsS~aAikK~i~~~Y~g~~v~----k~n~~lk~alK~ 95 (243)
T KOG4012|consen 43 AHPPYSEMITEAISALKERKGSSLAAIKKYIAANYPGDDVE----KNNSRLKLALKK 95 (243)
T ss_pred CCCcHHHHHHHHHHHhhhcccchHHHHHHHHhhcCccchhh----hhhHHHHHHHHh
Confidence 3445999999999975 445789999999999999877533 223455556544
No 17
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=57.76 E-value=8.1 Score=31.79 Aligned_cols=71 Identities=20% Similarity=0.218 Sum_probs=45.5
Q ss_pred CHHHHHHHHHhc--CCCCCCCHHHHHHHHHhcCCCCc--------cCC--CccccccccccccccccccccCCCCCCCCc
Q psy6883 149 SYIALITMAILQ--SPHKKLTLSGICEFIMSRFPYYR--------EKF--PAWQNSIRHNLSLNDCFVKIPREPGNPGKG 216 (414)
Q Consensus 149 SYaaLIa~AI~s--SP~kkLTLsEIYewI~~~FPYYr--------~~~--~GWQNSIRHNLSLNkcFvKVpR~~~~pGKG 216 (414)
+|-.|+...|.. .-.+.++.+||++.|.++|..=. ... .-|+|.|+=.++-=++.--|.+. ++|
T Consensus 1 ~~~~~~~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~~~~~~~sg~~~~~~~~ri~Wa~~~L~~aGli~~~----~rG 76 (92)
T PF14338_consen 1 TYDELMPPILEALKDLGGSASRKEIYERVAERFGLSDEERNERLPSGQGYSRFKNRIRWARSYLKKAGLIERP----KRG 76 (92)
T ss_pred CHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHhCCCHHHHHHHcccCCcchhHHHhHHHHHHHHHHCCCccCC----CCC
Confidence 355566555443 33589999999999999987431 111 25999998766654444333332 444
Q ss_pred eeEEecCc
Q psy6883 217 NYWTLDPM 224 (414)
Q Consensus 217 syWtLdP~ 224 (414)
+|+|-+.
T Consensus 77 -~~~iT~~ 83 (92)
T PF14338_consen 77 -IWRITEK 83 (92)
T ss_pred -ceEECHh
Confidence 9999874
No 18
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=44.92 E-value=16 Score=28.19 Aligned_cols=53 Identities=17% Similarity=0.217 Sum_probs=34.3
Q ss_pred HHHHHHHHHhcCC--CCCCCHHHHHHHHHhcCCCCccCCCcccccccccc-cccccc
Q psy6883 150 YIALITMAILQSP--HKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNL-SLNDCF 203 (414)
Q Consensus 150 YaaLIa~AI~sSP--~kkLTLsEIYewI~~~FPYYr~~~~GWQNSIRHNL-SLNkcF 203 (414)
-..+|..+|.+.. ++.+.|+++..++.++||-|....=|.. +++.=| ++-+.|
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 4578888885544 3489999999999999998876655543 333333 334443
No 19
>COG2958 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.67 E-value=27 Score=35.60 Aligned_cols=69 Identities=17% Similarity=0.190 Sum_probs=46.8
Q ss_pred CHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCC------ccCCCc------cccccccccccccccccccCCCCCCCCc
Q psy6883 149 SYIALITMAILQSPHKKLTLSGICEFIMSRFPYY------REKFPA------WQNSIRHNLSLNDCFVKIPREPGNPGKG 216 (414)
Q Consensus 149 SYaaLIa~AI~sSP~kkLTLsEIYewI~~~FPYY------r~~~~G------WQNSIRHNLSLNkcFvKVpR~~~~pGKG 216 (414)
+|..+|-..|+. .+.++|..|||+|+.+.||-= ....+. =--+.|-||-.+.-|.||... ..
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-SEEPFTAREIAEKAFETFPAECQEKKFDSGGDTPQQLVAEIIYTRPNLQEKHPFLKVTEG-----PR 79 (307)
T ss_pred hhHHHHHHHHHc-cCCCCcHHHHHHHHHHhccHHHHHHhhccccccHHHHHHHHHhcCccccccCcccccccC-----ce
Confidence 466666666665 789999999999999999842 111111 234567888889999998543 33
Q ss_pred eeEEecC
Q psy6883 217 NYWTLDP 223 (414)
Q Consensus 217 syWtLdP 223 (414)
-||--.-
T Consensus 80 ~~~lke~ 86 (307)
T COG2958 80 LYYLKEA 86 (307)
T ss_pred EEeeccc
Confidence 5665443
No 20
>KOG2236|consensus
Probab=22.20 E-value=2.6e+02 Score=30.72 Aligned_cols=17 Identities=41% Similarity=0.429 Sum_probs=9.5
Q ss_pred CCCCCCcccCCCCCCCC
Q psy6883 28 TSFDSPLDLRGAPHPGD 44 (414)
Q Consensus 28 ~~~~~~~~~~~~~~~~~ 44 (414)
.+-+.++||---+.-||
T Consensus 84 ~~~~~~~d~vd~~~~g~ 100 (483)
T KOG2236|consen 84 GSVDQPDDLVDPILVGD 100 (483)
T ss_pred CcccccccccchhhcCC
Confidence 45566677665544443
Done!