Query psy9499
Match_columns 289
No_of_seqs 214 out of 833
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 20:55:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9499.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9499hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3563|consensus 100.0 1.8E-41 3.9E-46 323.5 7.1 109 119-227 168-276 (454)
2 KOG3562|consensus 100.0 2.8E-40 6.1E-45 299.5 6.9 115 121-235 10-125 (277)
3 PF00250 Fork_head: Fork head 100.0 1.4E-39 3.1E-44 261.2 2.6 96 124-219 1-96 (96)
4 cd00059 FH Forkhead (FH), also 100.0 2.4E-38 5.1E-43 246.1 7.4 78 124-201 1-78 (78)
5 smart00339 FH FORKHEAD. FORKHE 100.0 2.7E-37 5.8E-42 245.1 7.2 87 124-210 1-87 (89)
6 KOG2294|consensus 100.0 2.5E-37 5.4E-42 296.8 -0.9 104 120-223 126-232 (454)
7 KOG4385|consensus 99.9 3.4E-24 7.4E-29 211.0 0.6 84 115-203 359-442 (581)
8 COG5025 Transcription factor o 99.8 1.5E-21 3.2E-26 198.5 5.0 101 114-214 327-427 (610)
9 COG5025 Transcription factor o 99.6 3.5E-16 7.5E-21 159.5 -0.7 90 122-211 84-173 (610)
10 PF00538 Linker_histone: linke 93.8 0.08 1.7E-06 40.6 3.6 33 128-160 4-37 (77)
11 smart00526 H15 Domain in histo 93.1 0.16 3.5E-06 37.6 4.3 32 128-159 6-38 (66)
12 cd00073 H15 linker histone 1 a 91.7 0.28 6.1E-06 38.6 4.2 34 128-161 6-40 (88)
13 PF05066 HARE-HTH: HB1, ASXL, 82.0 0.88 1.9E-05 34.1 1.7 58 127-186 1-63 (72)
14 KOG4012|consensus 71.9 4.1 9E-05 38.5 3.4 51 126-180 44-95 (243)
15 PF14338 Mrr_N: Mrr N-terminal 63.0 6.3 0.00014 30.9 2.4 72 128-204 1-84 (92)
16 COG2958 Uncharacterized protei 50.4 20 0.00044 34.7 3.9 70 128-203 6-87 (307)
17 PF12872 OST-HTH: OST-HTH/LOTU 37.7 31 0.00068 25.2 2.5 40 129-168 6-47 (74)
18 cd06649 PKc_MEK2 Catalytic dom 27.5 33 0.00071 31.6 1.4 49 129-182 277-328 (331)
19 KOG1528|consensus 27.4 26 0.00057 34.6 0.7 31 174-204 109-140 (351)
20 PF10264 Stork_head: Winged he 26.8 99 0.0022 24.7 3.8 46 129-177 12-59 (80)
21 PRK09462 fur ferric uptake reg 24.0 1.1E+02 0.0024 25.7 3.9 30 131-160 20-49 (148)
22 cd05071 PTKc_Src Catalytic dom 21.5 87 0.0019 27.4 2.8 33 126-158 229-261 (262)
No 1
>KOG3563|consensus
Probab=100.00 E-value=1.8e-41 Score=323.50 Aligned_cols=109 Identities=58% Similarity=1.058 Sum_probs=104.6
Q ss_pred CCCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeE
Q psy9499 119 KNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYW 198 (289)
Q Consensus 119 ~~~~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~W 198 (289)
.-.+.||||||+.||+|||+.+|.|+|||+|||+||++.|||||.+...|||||||.||+|+||+||+|.+++||||+||
T Consensus 168 sY~haKPPYSYISLITMAIQ~~pskmLTLSEIYqwIMDLFPyYrqNQQRWQNSIRHSLSFNDCFVKVaRSPDKPGKGSfW 247 (454)
T KOG3563|consen 168 SYTHAKPPYSYISLITMAIQQAPSKMLTLSEIYQWIMDLFPYYRQNQQRWQNSIRHSLSFNDCFVKVARSPDKPGKGSFW 247 (454)
T ss_pred cccCCCCChhHHHHHHHHHHhCCccceeHHHHHHHHHHhhhHhhhhHHHHHhhhhhhccccceeeeccCCCCCCCCccce
Confidence 34679999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EeCCCchhcccCccchhcccccCCCCCCc
Q psy9499 199 TLDPMAEDMFDNGSFLRRRKRYKRTPPDF 227 (289)
Q Consensus 199 tldP~~e~~f~~g~~~RrRkr~kr~~p~~ 227 (289)
+|+|++..|||||.|+||+||||...++.
T Consensus 248 TLHpdsGNMFENGCYLRRQKRFK~ekk~~ 276 (454)
T KOG3563|consen 248 TLHPDSGNMFENGCYLRRQKRFKCEKKEA 276 (454)
T ss_pred eecCCcCcccccchhehhhhhhhhhhhhc
Confidence 99999999999999999999999876654
No 2
>KOG3562|consensus
Probab=100.00 E-value=2.8e-40 Score=299.50 Aligned_cols=115 Identities=58% Similarity=1.029 Sum_probs=105.7
Q ss_pred CCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeEEe
Q psy9499 121 SIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTL 200 (289)
Q Consensus 121 ~~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~Wtl 200 (289)
..+||||||+.|.+|||++||+|+|.|+|||+||+++|||||.+.+.||||+|||||+|+||+||+|..+.+|||+||.|
T Consensus 10 ~dQKPPYSYIsLTaMAI~~SpekmLPLseIYkfImDrFPfYRkNTQrWQNSLRHNLSFNDCFIKiPRr~drpGKGsyWal 89 (277)
T KOG3562|consen 10 GDQKPPYSYISLTAMAIQSSPEKMLPLSEIYKFIMDRFPFYRKNTQRWQNSLRHNLSFNDCFIKIPRRPDRPGKGSYWAL 89 (277)
T ss_pred cccCCCceeeehhhHHhhcChhhcCcHHHHHHHHHhhCchhhhchHHHHHHhhccccccceeeecCCCCCCCCCccceee
Confidence 46999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCchhcccCccchhcccccCCCC-CCccCCCchhH
Q psy9499 201 DPMAEDMFDNGSFLRRRKRYKRTP-PDFLLRDPHAA 235 (289)
Q Consensus 201 dP~~e~~f~~g~~~RrRkr~kr~~-p~~~~r~~~~~ 235 (289)
+|.+.+|||||+++|||||+|..+ .+......+.+
T Consensus 90 HP~a~dMFENGS~LRRrKRFrv~k~~d~d~~n~~l~ 125 (277)
T KOG3562|consen 90 HPSAFDMFENGSLLRRRKRFRVLKSDDKDPSNTHLP 125 (277)
T ss_pred ccchhhhcccchHHHHhhhhhhccccccCccccccc
Confidence 999999999999999999998765 33333333333
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=1.4e-39 Score=261.16 Aligned_cols=96 Identities=66% Similarity=1.208 Sum_probs=89.7
Q ss_pred CCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeEEeCCC
Q psy9499 124 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPM 203 (289)
Q Consensus 124 KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~WtldP~ 203 (289)
||||||++||+|||+++|+++|||+|||+||+++||||+.+..+||||||||||+|+||+||++..+++|||+||+|+++
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 89999999999999999999999999999999999999999999999999999999999999998888999999999999
Q ss_pred chhcccCccchhcccc
Q psy9499 204 AEDMFDNGSFLRRRKR 219 (289)
Q Consensus 204 ~e~~f~~g~~~RrRkr 219 (289)
+...|+++.++|+|||
T Consensus 81 ~~~~~~~~~~~~~~~~ 96 (96)
T PF00250_consen 81 AIEEFEKGRFKRRRKR 96 (96)
T ss_dssp HHHHHHHSCCSSSSSS
T ss_pred HHHHHhcchhhhhhcc
Confidence 9999999998888765
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=2.4e-38 Score=246.06 Aligned_cols=78 Identities=69% Similarity=1.249 Sum_probs=76.7
Q ss_pred CCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeEEeC
Q psy9499 124 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLD 201 (289)
Q Consensus 124 KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~Wtld 201 (289)
||||||++||++||+++|+++|||+|||+||+++||||+.+..|||||||||||+|+||+||+|..+++|||+||+||
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=2.7e-37 Score=245.12 Aligned_cols=87 Identities=74% Similarity=1.277 Sum_probs=83.0
Q ss_pred CCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeEEeCCC
Q psy9499 124 KPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLDPM 203 (289)
Q Consensus 124 KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~WtldP~ 203 (289)
||||||++||++||+++|+++|||+|||+||+++||||+.+.+|||||||||||+|+||+||++..+.+|||+||+|+|+
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 chhcccC
Q psy9499 204 AEDMFDN 210 (289)
Q Consensus 204 ~e~~f~~ 210 (289)
++.+|+.
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=2.5e-37 Score=296.82 Aligned_cols=104 Identities=65% Similarity=1.146 Sum_probs=98.1
Q ss_pred CCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHh-cCCCcccCC-CccccccccccccccccccccCCCCCCCCcee
Q psy9499 120 NSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMS-RFPYYREKF-PAWQNSIRHNLSLNDCFVKIPREPGNPGKGNY 197 (289)
Q Consensus 120 ~~~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~-~fPyyr~~~-~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~ 197 (289)
...+||||||++||+|||+.+++|+|||+|||+||+. +|||||++. .|||||||||||||+||+||+|+.+.+|||+|
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-cccCccchhcccccCCC
Q psy9499 198 WTLDPMAED-MFDNGSFLRRRKRYKRT 223 (289)
Q Consensus 198 WtldP~~e~-~f~~g~~~RrRkr~kr~ 223 (289)
|+|||+.++ ||++|.|+|||+++++.
T Consensus 206 W~ldP~~~~~~~~~g~~~rr~~~~~~~ 232 (454)
T KOG2294|consen 206 WTLDPDDENNMFDNGSFRRRRRSKSNG 232 (454)
T ss_pred cccCcchhccccccccccccccccccc
Confidence 999999998 99999999988875543
No 7
>KOG4385|consensus
Probab=99.88 E-value=3.4e-24 Score=210.95 Aligned_cols=84 Identities=44% Similarity=0.841 Sum_probs=79.2
Q ss_pred ccCCCCCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCC
Q psy9499 115 KQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGK 194 (289)
Q Consensus 115 ~~~~~~~~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGK 194 (289)
.+..++..+||||+|+.||.+||+.+|++.|||+|||.|+.+.|.|||.+...|||+||||||||+||++|+. -|
T Consensus 359 ~dfyk~~dvRPPfTYAsLIRqAIlESpdkQLTLNEIY~WFTrtFAYFRRNaATWKnAVRHNLSLHKCF~RVEn-----vk 433 (581)
T KOG4385|consen 359 MDFYKNADVRPPFTYASLIRQAILESPDKQLTLNEIYNWFTRTFAYFRRNAATWKNAVRHNLSLHKCFVRVEN-----VK 433 (581)
T ss_pred hhhhhccccCCchhHHHHHHHHHhcCchhhccHHHHHHHHHHHHHHHhccchhHhHHHhhhhHHHHHHHHHHH-----Hh
Confidence 3467788899999999999999999999999999999999999999999999999999999999999999988 49
Q ss_pred ceeEEeCCC
Q psy9499 195 GNYWTLDPM 203 (289)
Q Consensus 195 G~~WtldP~ 203 (289)
|--|++|..
T Consensus 434 gavwtvDe~ 442 (581)
T KOG4385|consen 434 GAVWTVDER 442 (581)
T ss_pred cceeeeehh
Confidence 999999954
No 8
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.83 E-value=1.5e-21 Score=198.49 Aligned_cols=101 Identities=48% Similarity=0.722 Sum_probs=92.3
Q ss_pred CccCCCCCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCC
Q psy9499 114 DKQDGKNSIVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPG 193 (289)
Q Consensus 114 ~~~~~~~~~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pG 193 (289)
......+...||+++|+.||+.||+.+++++|+|.+||.||..+|||||.+..+||||||||||+|++|.||++..+.+|
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 34455678899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceeEEeCCCchhcccCccch
Q psy9499 194 KGNYWTLDPMAEDMFDNGSFL 214 (289)
Q Consensus 194 KG~~WtldP~~e~~f~~g~~~ 214 (289)
||+||+++.+....++.....
T Consensus 407 Kg~fw~i~~s~~~~~~sk~~~ 427 (610)
T COG5025 407 KGCFWKIDYSYIYEKESKRNP 427 (610)
T ss_pred CcccCccChhhhhhhcccccc
Confidence 999999999887666654433
No 9
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.56 E-value=3.5e-16 Score=159.54 Aligned_cols=90 Identities=48% Similarity=0.781 Sum_probs=84.8
Q ss_pred CCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccccccccccccCCCCCCCCceeEEeC
Q psy9499 122 IVKPPYSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLNDCFVKIPREPGNPGKGNYWTLD 201 (289)
Q Consensus 122 ~~KPPySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG~~Wtld 201 (289)
..||||+|+.+|.++|++++++.|||..||.||-..|.||.....+|||||||||++|++|.||.+..+..+||.||.+.
T Consensus 84 ~~v~~~s~a~gr~~~il~s~~~~lt~s~~~~~~~~~~~~~~k~~~~~~~sIr~Nls~~~a~~~i~g~~g~~~~g~~~~ig 163 (610)
T COG5025 84 YYVPPYSYATGRGLAILNSPDKPLTLSKIYTWIHNTFFYYAKVVSRWQNSIRHNLSLNDAFIKIEGRNGAKVKGHFWSIG 163 (610)
T ss_pred cccCCeeeeeccccccccCcccCCcccceeeeeeecccccccccchhhhhhhcccccCceEEEEeccCCccccceeeccC
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCchhcccCc
Q psy9499 202 PMAEDMFDNG 211 (289)
Q Consensus 202 P~~e~~f~~g 211 (289)
|+.+..|...
T Consensus 164 P~~~~~~l~~ 173 (610)
T COG5025 164 PGHETQFLKS 173 (610)
T ss_pred CCccceeecc
Confidence 9887666433
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=93.75 E-value=0.08 Score=40.55 Aligned_cols=33 Identities=24% Similarity=0.356 Sum_probs=28.9
Q ss_pred CHHHHHHHHHhcCC-CCCCCHHHHHHHHHhcCCC
Q psy9499 128 SYIALITMAILQSP-HKKLTLSGICEFIMSRFPY 160 (289)
Q Consensus 128 SYa~LI~~AI~sSp-~k~LTL~eIY~~I~~~fPy 160 (289)
+|..||.+||.+.. .+..+++.|..||+.+|+.
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 49999999999844 4789999999999999964
No 11
>smart00526 H15 Domain in histone families 1 and 5.
Probab=93.14 E-value=0.16 Score=37.63 Aligned_cols=32 Identities=28% Similarity=0.388 Sum_probs=28.2
Q ss_pred CHHHHHHHHHhcCCC-CCCCHHHHHHHHHhcCC
Q psy9499 128 SYIALITMAILQSPH-KKLTLSGICEFIMSRFP 159 (289)
Q Consensus 128 SYa~LI~~AI~sSp~-k~LTL~eIY~~I~~~fP 159 (289)
+|..||.+||....+ +..+++.|..||+.+|.
T Consensus 6 ~~~~mI~eAI~~l~er~GsS~~aI~kyi~~~~~ 38 (66)
T smart00526 6 PYSEMITEAISALKERKGSSLQAIKKYIEANYK 38 (66)
T ss_pred CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCC
Confidence 799999999998544 67999999999999965
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=91.67 E-value=0.28 Score=38.63 Aligned_cols=34 Identities=24% Similarity=0.366 Sum_probs=29.6
Q ss_pred CHHHHHHHHHhc-CCCCCCCHHHHHHHHHhcCCCc
Q psy9499 128 SYIALITMAILQ-SPHKKLTLSGICEFIMSRFPYY 161 (289)
Q Consensus 128 SYa~LI~~AI~s-Sp~k~LTL~eIY~~I~~~fPyy 161 (289)
+|..||.+||.. ...+..+++.|..||+.+|+.-
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 699999999997 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=82.03 E-value=0.88 Score=34.08 Aligned_cols=58 Identities=19% Similarity=0.198 Sum_probs=37.4
Q ss_pred CCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccc-----ccccccccc
Q psy9499 127 YSYIALITMAILQSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLS-----LNDCFVKIP 186 (289)
Q Consensus 127 ySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLS-----lNkcF~Kvp 186 (289)
+||..++...|+... +.|+.+||++.|.+.--| ....+...++|+-.|. .+..|++|.
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 899999999999976543 3235567777773333 455899874
No 14
>KOG4012|consensus
Probab=71.89 E-value=4.1 Score=38.48 Aligned_cols=51 Identities=27% Similarity=0.322 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHHhcCCC-CCCCHHHHHHHHHhcCCCcccCCCcccccccccccccc
Q psy9499 126 PYSYIALITMAILQSPH-KKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLSLND 180 (289)
Q Consensus 126 PySYa~LI~~AI~sSp~-k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLSlNk 180 (289)
.-+|+.||.+||...-+ ....+.-|+.||..+|+.|.-.. |.-|.+++|+.
T Consensus 44 ~P~~~~mi~eAi~a~keR~GsS~aAikK~i~~~Y~g~~v~k----~n~~lk~alK~ 95 (243)
T KOG4012|consen 44 HPPYSEMITEAISALKERKGSSLAAIKKYIAANYPGDDVEK----NNSRLKLALKK 95 (243)
T ss_pred CCcHHHHHHHHHHHhhhcccchHHHHHHHHhhcCccchhhh----hhHHHHHHHHh
Confidence 34599999999998554 67899999999999998775422 23355556543
No 15
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=63.03 E-value=6.3 Score=30.85 Aligned_cols=72 Identities=21% Similarity=0.254 Sum_probs=45.7
Q ss_pred CHHHHHHHHHhc--CCCCCCCHHHHHHHHHhcCCCcc--------cCC--CccccccccccccccccccccCCCCCCCCc
Q psy9499 128 SYIALITMAILQ--SPHKKLTLSGICEFIMSRFPYYR--------EKF--PAWQNSIRHNLSLNDCFVKIPREPGNPGKG 195 (289)
Q Consensus 128 SYa~LI~~AI~s--Sp~k~LTL~eIY~~I~~~fPyyr--------~~~--~gWqNSIRHNLSlNkcF~Kvpr~~~~pGKG 195 (289)
+|-.|+...|.. .-.+.++.+||++.|.++|..=. ... .-|+|.|+=.++-=++.--|.+ +++|
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 355566555543 33688999999999999987431 111 2599999866654444333333 3445
Q ss_pred eeEEeCCCc
Q psy9499 196 NYWTLDPMA 204 (289)
Q Consensus 196 ~~WtldP~~ 204 (289)
+|.|-+.-
T Consensus 77 -~~~iT~~G 84 (92)
T PF14338_consen 77 -IWRITEKG 84 (92)
T ss_pred -ceEECHhH
Confidence 99997654
No 16
>COG2958 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.43 E-value=20 Score=34.69 Aligned_cols=70 Identities=19% Similarity=0.219 Sum_probs=48.0
Q ss_pred CHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCc------ccCCCc------cccccccccccccccccccCCCCCCCCc
Q psy9499 128 SYIALITMAILQSPHKKLTLSGICEFIMSRFPYY------REKFPA------WQNSIRHNLSLNDCFVKIPREPGNPGKG 195 (289)
Q Consensus 128 SYa~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyy------r~~~~g------WqNSIRHNLSlNkcF~Kvpr~~~~pGKG 195 (289)
+|..+|-..|+. .+..+|..|||+|+.+.||-= ....+. =--+.|-||-.+.-|.||.. |..
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 788999999999999999843 111111 23456788888999999854 344
Q ss_pred eeEEeCCC
Q psy9499 196 NYWTLDPM 203 (289)
Q Consensus 196 ~~WtldP~ 203 (289)
-||--+-+
T Consensus 80 ~~~lke~~ 87 (307)
T COG2958 80 LYYLKEAA 87 (307)
T ss_pred EEeecccc
Confidence 57765443
No 17
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=37.70 E-value=31 Score=25.18 Aligned_cols=40 Identities=10% Similarity=0.149 Sum_probs=29.3
Q ss_pred HHHHHHHHHhcCC--CCCCCHHHHHHHHHhcCCCcccCCCcc
Q psy9499 129 YIALITMAILQSP--HKKLTLSGICEFIMSRFPYYREKFPAW 168 (289)
Q Consensus 129 Ya~LI~~AI~sSp--~k~LTL~eIY~~I~~~fPyyr~~~~gW 168 (289)
-..+|..+|.+.. ++.+.|+++-.++.++||-|....=|.
T Consensus 6 ~~~~l~~ll~~~~~~~g~v~ls~l~~~~~~~~~~f~~~~yG~ 47 (74)
T PF12872_consen 6 LKKLLRELLESQKGEDGWVSLSQLGQEYKKKYPDFDPRDYGF 47 (74)
T ss_dssp HHHHHHHHHHHTCTTTSSEEHHHHHHHHHHHHTT--TCCTTS
T ss_pred HHHHHHHHHHhCcCCCceEEHHHHHHHHHHHCCCCCccccCC
Confidence 4578888885544 357999999999999998887665443
No 18
>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=27.54 E-value=33 Score=31.57 Aligned_cols=49 Identities=10% Similarity=0.268 Sum_probs=39.9
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCCcccC---CCcccccccccccccccc
Q psy9499 129 YIALITMAILQSPHKKLTLSGICEFIMSRFPYYREK---FPAWQNSIRHNLSLNDCF 182 (289)
Q Consensus 129 Ya~LI~~AI~sSp~k~LTL~eIY~~I~~~fPyyr~~---~~gWqNSIRHNLSlNkcF 182 (289)
+..||...+.-.|++|.|..||.+ .|||+.. ...|++.+.-+|+++.-+
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 678999999999999999999975 4777643 456899999888887543
No 19
>KOG1528|consensus
Probab=27.40 E-value=26 Score=34.61 Aligned_cols=31 Identities=35% Similarity=0.590 Sum_probs=23.1
Q ss_pred cccccccccccccCCCCCC-CCceeEEeCCCc
Q psy9499 174 HNLSLNDCFVKIPREPGNP-GKGNYWTLDPMA 204 (289)
Q Consensus 174 HNLSlNkcF~Kvpr~~~~p-GKG~~WtldP~~ 204 (289)
.-||..+...-+.+...+. .||.+|.|||-.
T Consensus 109 ~~ls~~dvl~aID~G~s~GG~kGrhWvLDPID 140 (351)
T KOG1528|consen 109 SPLSSDDVLKAIDRGNSEGGPKGRHWVLDPID 140 (351)
T ss_pred CCCCHHHHHHHHhcccccCCCCCceEEeccCC
Confidence 3477777777777765554 489999999954
No 20
>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=26.77 E-value=99 Score=24.71 Aligned_cols=46 Identities=13% Similarity=0.148 Sum_probs=34.4
Q ss_pred HHHHHHHHHh--cCCCCCCCHHHHHHHHHhcCCCcccCCCccccccccccc
Q psy9499 129 YIALITMAIL--QSPHKKLTLSGICEFIMSRFPYYREKFPAWQNSIRHNLS 177 (289)
Q Consensus 129 Ya~LI~~AI~--sSp~k~LTL~eIY~~I~~~fPyyr~~~~gWqNSIRHNLS 177 (289)
-...|+.||. ++.+...|+..|.+++.++||--.. -=+..|++.|.
T Consensus 12 L~EvlC~~I~dln~~~~~at~E~l~~~L~~~yp~i~~---Ps~e~l~~~L~ 59 (80)
T PF10264_consen 12 LPEVLCWVISDLNAAGQPATQETLREHLRKHYPGIAI---PSQEVLYNTLG 59 (80)
T ss_pred HHHHHHHHHHHHhccCCcchHHHHHHHHHHhCCCCCC---CCHHHHHHHHH
Confidence 4578888887 5888999999999999999995432 12345555554
No 21
>PRK09462 fur ferric uptake regulator; Provisional
Probab=23.96 E-value=1.1e+02 Score=25.70 Aligned_cols=30 Identities=3% Similarity=0.013 Sum_probs=24.1
Q ss_pred HHHHHHHhcCCCCCCCHHHHHHHHHhcCCC
Q psy9499 131 ALITMAILQSPHKKLTLSGICEFIMSRFPY 160 (289)
Q Consensus 131 ~LI~~AI~sSp~k~LTL~eIY~~I~~~fPy 160 (289)
..|..+|.+..++-+|..|||+.+.+..|-
T Consensus 20 ~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~ 49 (148)
T PRK09462 20 LKILEVLQEPDNHHVSAEDLYKRLIDMGEE 49 (148)
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHHHhhCCC
Confidence 456667776667789999999999988874
No 22
>cd05071 PTKc_Src Catalytic domain of the Protein Tyrosine Kinase, Src. Protein Tyrosine Kinase (PTK) family; Src kinase; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Src (or c-Src) is a cytoplasmic (or non-receptor) tyr kinase, containing an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region with a conserved tyr. It is activated by autophosphorylation at the tyr kinase domain, and is negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). c-Src is the vertebrate homolog of the oncogenic protein (v-Src) from Rous sarcoma virus. Together with other Src subfamily proteins, it is invo
Probab=21.54 E-value=87 Score=27.38 Aligned_cols=33 Identities=21% Similarity=0.325 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcC
Q psy9499 126 PYSYIALITMAILQSPHKKLTLSGICEFIMSRF 158 (289)
Q Consensus 126 PySYa~LI~~AI~sSp~k~LTL~eIY~~I~~~f 158 (289)
+-....||..++...|++|.|.++|.+++++-|
T Consensus 229 ~~~l~~li~~~l~~~p~~Rp~~~~~~~~l~~~~ 261 (262)
T cd05071 229 PESLHDLMCQCWRKEPEERPTFEYLQAFLEDYF 261 (262)
T ss_pred CHHHHHHHHHHccCCcccCCCHHHHHHHHHHhc
Confidence 345788999999999999999999999998765
Done!