Query psy723
Match_columns 395
No_of_seqs 204 out of 831
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 21:24:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy723.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/723hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3563|consensus 100.0 7.7E-46 1.7E-50 366.3 12.0 106 95-200 170-277 (454)
2 KOG3562|consensus 100.0 5.8E-38 1.3E-42 295.2 8.5 105 95-199 10-116 (277)
3 PF00250 Fork_head: Fork head 100.0 7.5E-37 1.6E-41 254.9 1.2 93 98-190 1-95 (96)
4 cd00059 FH Forkhead (FH), also 100.0 1E-35 2.2E-40 240.3 6.9 76 98-173 1-78 (78)
5 smart00339 FH FORKHEAD. FORKHE 100.0 1.5E-34 3.2E-39 238.3 6.8 85 98-182 1-87 (89)
6 KOG2294|consensus 100.0 1.2E-33 2.7E-38 281.2 -0.2 99 95-193 127-230 (454)
7 KOG4385|consensus 100.0 2.9E-31 6.3E-36 270.1 4.1 145 3-175 298-442 (581)
8 COG5025 Transcription factor o 99.8 4E-20 8.6E-25 195.3 2.8 93 94-186 333-427 (610)
9 COG5025 Transcription factor o 99.5 4.7E-15 1E-19 157.2 -1.4 93 95-187 83-177 (610)
10 PF00538 Linker_histone: linke 91.4 0.23 5E-06 39.7 3.5 33 102-134 4-37 (77)
11 smart00526 H15 Domain in histo 90.3 0.58 1.3E-05 36.2 4.7 32 102-133 6-38 (66)
12 cd00073 H15 linker histone 1 a 86.1 1.1 2.3E-05 36.9 4.0 33 102-134 6-39 (88)
13 PF09354 HNF_C: HNF3 C-termina 81.6 0.52 1.1E-05 37.9 0.3 10 314-323 1-10 (65)
14 KOG4012|consensus 72.8 3.3 7.2E-05 40.8 3.2 66 100-173 44-115 (243)
15 PF05066 HARE-HTH: HB1, ASXL, 70.2 1.3 2.9E-05 34.6 -0.2 58 101-160 1-63 (72)
16 PF14338 Mrr_N: Mrr N-terminal 41.2 22 0.00047 29.1 2.3 71 102-175 1-83 (92)
17 PF03373 Octapeptide: Octapept 33.6 20 0.00044 18.4 0.6 8 329-336 1-8 (8)
18 COG2958 Uncharacterized protei 30.1 49 0.0011 33.6 3.1 67 102-172 6-84 (307)
19 PF10264 Stork_head: Winged he 24.2 1.1E+02 0.0023 25.8 3.6 33 103-135 12-46 (80)
20 PF12872 OST-HTH: OST-HTH/LOTU 23.7 71 0.0015 24.4 2.4 53 103-156 6-61 (74)
No 1
>KOG3563|consensus
Probab=100.00 E-value=7.7e-46 Score=366.33 Aligned_cols=106 Identities=44% Similarity=0.851 Sum_probs=101.5
Q ss_pred CCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCccccCCCCccccccccccccchhcccCcC--CCCCcceeee
Q psy723 95 EEPKPQHSYIGLIAMAILSSPEMKLVLSDIYQYILDNYSYFRTRGPGWRNSIRHNLSLNDCFIKAGRS--ANGKGHYWSI 172 (395)
Q Consensus 95 ~~~KPPySYa~LI~~AI~sSP~kkLTLsEIY~~I~~~fPYyR~~~~gWKNSIRHNLSlN~~FvKv~R~--~~GKG~~Wtl 172 (395)
...||||||+.||.|||+.+|.|+|||+|||+||++-|||||.+...|||||||.||+|+||+||.|. .+|||+||+|
T Consensus 170 ~haKPPYSYISLITMAIQ~~pskmLTLSEIYqwIMDLFPyYrqNQQRWQNSIRHSLSFNDCFVKVaRSPDKPGKGSfWTL 249 (454)
T KOG3563|consen 170 THAKPPYSYISLITMAIQQAPSKMLTLSEIYQWIMDLFPYYRQNQQRWQNSIRHSLSFNDCFVKVARSPDKPGKGSFWTL 249 (454)
T ss_pred cCCCCChhHHHHHHHHHHhCCccceeHHHHHHHHHHhhhHhhhhHHHHHhhhhhhccccceeeeccCCCCCCCCccceee
Confidence 35799999999999999999999999999999999999999999999999999999999999999996 4899999999
Q ss_pred cCCchhhhccccchhhhhHHHHhhhcCC
Q psy723 173 HPANVDDFKKGDFRRRKAQRKVRRHMGL 200 (395)
Q Consensus 173 dP~~~~~f~~g~~rRRk~~rk~rk~~~~ 200 (395)
+|++.++|++|.+.||.||.|+.|+.+.
T Consensus 250 HpdsGNMFENGCYLRRQKRFK~ekk~~~ 277 (454)
T KOG3563|consen 250 HPDSGNMFENGCYLRRQKRFKCEKKEAS 277 (454)
T ss_pred cCCcCcccccchhehhhhhhhhhhhhcc
Confidence 9999999999999999999999887764
No 2
>KOG3562|consensus
Probab=100.00 E-value=5.8e-38 Score=295.20 Aligned_cols=105 Identities=48% Similarity=0.894 Sum_probs=100.5
Q ss_pred CCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCccccCCCCccccccccccccchhcccCcC--CCCCcceeee
Q psy723 95 EEPKPQHSYIGLIAMAILSSPEMKLVLSDIYQYILDNYSYFRTRGPGWRNSIRHNLSLNDCFIKAGRS--ANGKGHYWSI 172 (395)
Q Consensus 95 ~~~KPPySYa~LI~~AI~sSP~kkLTLsEIY~~I~~~fPYyR~~~~gWKNSIRHNLSlN~~FvKv~R~--~~GKG~~Wtl 172 (395)
.++||||||+.|.+|||.+||+|+|.|+|||+||+++|||||.+...||||+|||||+|+||+||+|+ ..|||+||+|
T Consensus 10 ~dQKPPYSYIsLTaMAI~~SpekmLPLseIYkfImDrFPfYRkNTQrWQNSLRHNLSFNDCFIKiPRr~drpGKGsyWal 89 (277)
T KOG3562|consen 10 GDQKPPYSYISLTAMAIQSSPEKMLPLSEIYKFIMDRFPFYRKNTQRWQNSLRHNLSFNDCFIKIPRRPDRPGKGSYWAL 89 (277)
T ss_pred cccCCCceeeehhhHHhhcChhhcCcHHHHHHHHHhhCchhhhchHHHHHHhhccccccceeeecCCCCCCCCCccceee
Confidence 57999999999999999999999999999999999999999999999999999999999999999997 4799999999
Q ss_pred cCCchhhhccccchhhhhHHHHhhhcC
Q psy723 173 HPANVDDFKKGDFRRRKAQRKVRRHMG 199 (395)
Q Consensus 173 dP~~~~~f~~g~~rRRk~~rk~rk~~~ 199 (395)
+|.+.++|++|.+.||+|+.++++...
T Consensus 90 HP~a~dMFENGS~LRRrKRFrv~k~~d 116 (277)
T KOG3562|consen 90 HPSAFDMFENGSLLRRRKRFRVLKSDD 116 (277)
T ss_pred ccchhhhcccchHHHHhhhhhhccccc
Confidence 999999999999999999999987543
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=7.5e-37 Score=254.86 Aligned_cols=93 Identities=57% Similarity=1.106 Sum_probs=86.3
Q ss_pred CCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCccccCCCCccccccccccccchhcccCc--CCCCCcceeeecCC
Q psy723 98 KPQHSYIGLIAMAILSSPEMKLVLSDIYQYILDNYSYFRTRGPGWRNSIRHNLSLNDCFIKAGR--SANGKGHYWSIHPA 175 (395)
Q Consensus 98 KPPySYa~LI~~AI~sSP~kkLTLsEIY~~I~~~fPYyR~~~~gWKNSIRHNLSlN~~FvKv~R--~~~GKG~~WtldP~ 175 (395)
||||||++||++||++||+++|||+|||+||+.+||||+.+..|||||||||||+|+||+||++ +..|||+||+|+|+
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 8999999999999999999999999999999999999999999999999999999999999999 45799999999999
Q ss_pred chhhhccccchhhhh
Q psy723 176 NVDDFKKGDFRRRKA 190 (395)
Q Consensus 176 ~~~~f~~g~~rRRk~ 190 (395)
+...|+++.+++|++
T Consensus 81 ~~~~~~~~~~~~~~~ 95 (96)
T PF00250_consen 81 AIEEFEKGRFKRRRK 95 (96)
T ss_dssp HHHHHHHSCCSSSSS
T ss_pred HHHHHhcchhhhhhc
Confidence 999999999987765
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=1e-35 Score=240.34 Aligned_cols=76 Identities=61% Similarity=1.090 Sum_probs=74.2
Q ss_pred CCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCccccCCCCccccccccccccchhcccCcC--CCCCcceeeec
Q psy723 98 KPQHSYIGLIAMAILSSPEMKLVLSDIYQYILDNYSYFRTRGPGWRNSIRHNLSLNDCFIKAGRS--ANGKGHYWSIH 173 (395)
Q Consensus 98 KPPySYa~LI~~AI~sSP~kkLTLsEIY~~I~~~fPYyR~~~~gWKNSIRHNLSlN~~FvKv~R~--~~GKG~~Wtld 173 (395)
||||||++||++||+++|+++|||+|||+||+++|||||.+..|||||||||||+|+||+||+|. ..|||+||+||
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 89999999999999999999999999999999999999999999999999999999999999998 67999999996
No 5
>smart00339 FH FORKHEAD. FORKHEAD, also known as a "winged helix"
Probab=100.00 E-value=1.5e-34 Score=238.29 Aligned_cols=85 Identities=58% Similarity=1.077 Sum_probs=80.2
Q ss_pred CCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCccccCCCCccccccccccccchhcccCcC--CCCCcceeeecCC
Q psy723 98 KPQHSYIGLIAMAILSSPEMKLVLSDIYQYILDNYSYFRTRGPGWRNSIRHNLSLNDCFIKAGRS--ANGKGHYWSIHPA 175 (395)
Q Consensus 98 KPPySYa~LI~~AI~sSP~kkLTLsEIY~~I~~~fPYyR~~~~gWKNSIRHNLSlN~~FvKv~R~--~~GKG~~WtldP~ 175 (395)
||||||++||++||+++|+++|||+|||+||+++|||||.+..|||||||||||+|+||+||+|. ..|||+||+|+|+
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 89999999999999999999999999999999999999999999999999999999999999985 4699999999999
Q ss_pred chhhhcc
Q psy723 176 NVDDFKK 182 (395)
Q Consensus 176 ~~~~f~~ 182 (395)
+...|..
T Consensus 81 ~~~~~~~ 87 (89)
T smart00339 81 AENMFEN 87 (89)
T ss_pred HHHHHhc
Confidence 8775544
No 6
>KOG2294|consensus
Probab=99.97 E-value=1.2e-33 Score=281.23 Aligned_cols=99 Identities=52% Similarity=0.978 Sum_probs=92.1
Q ss_pred CCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHh-cCCccccCC-CCccccccccccccchhcccCcCC--CCCccee
Q psy723 95 EEPKPQHSYIGLIAMAILSSPEMKLVLSDIYQYILD-NYSYFRTRG-PGWRNSIRHNLSLNDCFIKAGRSA--NGKGHYW 170 (395)
Q Consensus 95 ~~~KPPySYa~LI~~AI~sSP~kkLTLsEIY~~I~~-~fPYyR~~~-~gWKNSIRHNLSlN~~FvKv~R~~--~GKG~~W 170 (395)
..+||||||++||+|||+.|++|+|||+|||+||+. +|||||+++ .|||||||||||||+||+||+|.. .|||+||
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 999999999999999999999964 5999999
Q ss_pred eecCCchh-hhccccchhhhhHHH
Q psy723 171 SIHPANVD-DFKKGDFRRRKAQRK 193 (395)
Q Consensus 171 tldP~~~~-~f~~g~~rRRk~~rk 193 (395)
+|+|++.+ +|++|.++||+++.+
T Consensus 207 ~ldP~~~~~~~~~g~~~rr~~~~~ 230 (454)
T KOG2294|consen 207 TLDPDDENNMFDNGSFRRRRRSKS 230 (454)
T ss_pred ccCcchhccccccccccccccccc
Confidence 99999998 899999988776543
No 7
>KOG4385|consensus
Probab=99.96 E-value=2.9e-31 Score=270.09 Aligned_cols=145 Identities=29% Similarity=0.579 Sum_probs=138.4
Q ss_pred CccccCCCCCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCcccccccccchhhhhhhhhccCCCCCCCCCCCCCCcccc
Q psy723 3 SVSDKSQTEINSPPGSPADQNEPLGNATALVPTLDSHPLLPIEQYRIQLYNYAIQAERLRLSQQYGTPYTNYQTPNVNRV 82 (395)
Q Consensus 3 ~~~~~~~~~~~~~~~s~~~~~~~i~~~t~~i~~~~~~~~~~~~~~~~~ly~~~~~~er~r~~~~~~~p~~~~~~~~~~~~ 82 (395)
+++++||+++.+++++++.|++|+..|+++|+++..+++++. |+|..+++..|++.+.+.+.++|
T Consensus 298 s~~sss~qs~~~~atgs~gPl~p~~~gp~~~~t~~~pds~p~---------------rrR~sDk~~~Pisseia~N~dfy 362 (581)
T KOG4385|consen 298 SAASSSPQSLPQQATGSTGPLTPATQGPSVITTASAPDSGPA---------------RRRHSDKYNGPISSEIAQNMDFY 362 (581)
T ss_pred hhhhcCCCcccccCCCCCCcccccccCCCccccccCCCccch---------------hhcccccccCchhHHhhhhhhhh
Confidence 688999999999999999999999999999999999999987 99999999999999999999988
Q ss_pred cccCCCCcCCCCCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCccccCCCCccccccccccccchhcccCcC
Q psy723 83 MNYFHPRFQISSEEPKPQHSYIGLIAMAILSSPEMKLVLSDIYQYILDNYSYFRTRGPGWRNSIRHNLSLNDCFIKAGRS 162 (395)
Q Consensus 83 ~~~~~p~~~~~~~~~KPPySYa~LI~~AI~sSP~kkLTLsEIY~~I~~~fPYyR~~~~gWKNSIRHNLSlN~~FvKv~R~ 162 (395)
++ .+++|||+|+.||++||++||+|.|||+|||.|+...|.|||.+...|||+|||||||++||++|+
T Consensus 363 k~----------~dvRPPfTYAsLIRqAIlESpdkQLTLNEIY~WFTrtFAYFRRNaATWKnAVRHNLSLHKCF~RVE-- 430 (581)
T KOG4385|consen 363 KN----------ADVRPPFTYASLIRQAILESPDKQLTLNEIYNWFTRTFAYFRRNAATWKNAVRHNLSLHKCFVRVE-- 430 (581)
T ss_pred hc----------cccCCchhHHHHHHHHHhcCchhhccHHHHHHHHHHHHHHHhccchhHhHHHhhhhHHHHHHHHHH--
Confidence 77 899999999999999999999999999999999999999999999999999999999999999987
Q ss_pred CCCCcceeeecCC
Q psy723 163 ANGKGHYWSIHPA 175 (395)
Q Consensus 163 ~~GKG~~WtldP~ 175 (395)
.-||.-|++|..
T Consensus 431 -nvkgavwtvDe~ 442 (581)
T KOG4385|consen 431 -NVKGAVWTVDER 442 (581)
T ss_pred -HHhcceeeeehh
Confidence 479999999854
No 8
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.78 E-value=4e-20 Score=195.28 Aligned_cols=93 Identities=43% Similarity=0.705 Sum_probs=86.7
Q ss_pred CCCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCccccCCCCccccccccccccchhcccCcC--CCCCcceee
Q psy723 94 SEEPKPQHSYIGLIAMAILSSPEMKLVLSDIYQYILDNYSYFRTRGPGWRNSIRHNLSLNDCFIKAGRS--ANGKGHYWS 171 (395)
Q Consensus 94 ~~~~KPPySYa~LI~~AI~sSP~kkLTLsEIY~~I~~~fPYyR~~~~gWKNSIRHNLSlN~~FvKv~R~--~~GKG~~Wt 171 (395)
....||+++|+.||+.||+.+++++|+|++||.||..+|||||....+|+||||||||+|++|.||+|+ .+|||+||.
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 457899999999999999999999999999999999999999999999999999999999999999997 589999999
Q ss_pred ecCCchhhhccccch
Q psy723 172 IHPANVDDFKKGDFR 186 (395)
Q Consensus 172 ldP~~~~~f~~g~~r 186 (395)
|+.++...+...+.+
T Consensus 413 i~~s~~~~~~sk~~~ 427 (610)
T COG5025 413 IDYSYIYEKESKRNP 427 (610)
T ss_pred cChhhhhhhcccccc
Confidence 999998877765543
No 9
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.46 E-value=4.7e-15 Score=157.18 Aligned_cols=93 Identities=43% Similarity=0.694 Sum_probs=85.8
Q ss_pred CCCCCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCccccCCCCccccccccccccchhcccCcCC--CCCcceeee
Q psy723 95 EEPKPQHSYIGLIAMAILSSPEMKLVLSDIYQYILDNYSYFRTRGPGWRNSIRHNLSLNDCFIKAGRSA--NGKGHYWSI 172 (395)
Q Consensus 95 ~~~KPPySYa~LI~~AI~sSP~kkLTLsEIY~~I~~~fPYyR~~~~gWKNSIRHNLSlN~~FvKv~R~~--~GKG~~Wtl 172 (395)
..-||||+|+.+|.++|+.++.++|||..||.||-..|.||.....+|+|+|||||++++.|.|+.+.. .|||+||.|
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 457999999999999999999999999999999999999999999999999999999999999998764 599999999
Q ss_pred cCCchhhhccccchh
Q psy723 173 HPANVDDFKKGDFRR 187 (395)
Q Consensus 173 dP~~~~~f~~g~~rR 187 (395)
.|+....|..++.++
T Consensus 163 gP~~~~~~l~~g~~~ 177 (610)
T COG5025 163 GPGHETQFLKSGLRL 177 (610)
T ss_pred CCCccceeecccccc
Confidence 999888887766543
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=91.43 E-value=0.23 Score=39.72 Aligned_cols=33 Identities=30% Similarity=0.356 Sum_probs=29.0
Q ss_pred CHHHHHHHHHhcCCC-CCCCHHHHHHHHHhcCCc
Q psy723 102 SYIGLIAMAILSSPE-MKLVLSDIYQYILDNYSY 134 (395)
Q Consensus 102 SYa~LI~~AI~sSP~-kkLTLsEIY~~I~~~fPY 134 (395)
+|..||..||.+..+ +..++..|..||+.+|+.
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 499999999988665 569999999999999964
No 11
>smart00526 H15 Domain in histone families 1 and 5.
Probab=90.34 E-value=0.58 Score=36.21 Aligned_cols=32 Identities=38% Similarity=0.453 Sum_probs=28.3
Q ss_pred CHHHHHHHHHhcCCCCC-CCHHHHHHHHHhcCC
Q psy723 102 SYIGLIAMAILSSPEMK-LVLSDIYQYILDNYS 133 (395)
Q Consensus 102 SYa~LI~~AI~sSP~kk-LTLsEIY~~I~~~fP 133 (395)
+|..||..||.+..++. .++..|..||+.+|+
T Consensus 6 ~~~~mI~eAI~~l~er~GsS~~aI~kyi~~~~~ 38 (66)
T smart00526 6 PYSEMITEAISALKERKGSSLQAIKKYIEANYK 38 (66)
T ss_pred CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCC
Confidence 79999999998876644 999999999999965
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=86.15 E-value=1.1 Score=36.94 Aligned_cols=33 Identities=27% Similarity=0.349 Sum_probs=28.2
Q ss_pred CHHHHHHHHHhcCCC-CCCCHHHHHHHHHhcCCc
Q psy723 102 SYIGLIAMAILSSPE-MKLVLSDIYQYILDNYSY 134 (395)
Q Consensus 102 SYa~LI~~AI~sSP~-kkLTLsEIY~~I~~~fPY 134 (395)
+|..||..||.+-.+ +..++..|..||+.+|+.
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 699999999977444 458999999999999885
No 13
>PF09354 HNF_C: HNF3 C-terminal domain; InterPro: IPR018533 This presumed domain is found in the C-terminal region of Hepatocyte Nuclear Factor 3 alpha and beta chains. Its specific function is uncertain. The N-terminal region of this presumed domain contains an EH1 (engrailed homology 1) motif, that is characterised by the FxIxxIL sequence [].
Probab=81.64 E-value=0.52 Score=37.88 Aligned_cols=10 Identities=30% Similarity=0.418 Sum_probs=8.6
Q ss_pred cccccccHHH
Q psy723 314 KHAASITDEV 323 (395)
Q Consensus 314 ~hp~si~~~~ 323 (395)
||||||||-.
T Consensus 1 nHPFSI~nLm 10 (65)
T PF09354_consen 1 NHPFSINNLM 10 (65)
T ss_pred CCCcchhhhc
Confidence 7999999854
No 14
>KOG4012|consensus
Probab=72.83 E-value=3.3 Score=40.84 Aligned_cols=66 Identities=29% Similarity=0.365 Sum_probs=44.8
Q ss_pred CCCHHHHHHHHHhcCCCCC-CCHHHHHHHHHhcCCccccCCCCccccccccccccc-----hhcccCcCCCCCcceeeec
Q psy723 100 QHSYIGLIAMAILSSPEMK-LVLSDIYQYILDNYSYFRTRGPGWRNSIRHNLSLND-----CFIKAGRSANGKGHYWSIH 173 (395)
Q Consensus 100 PySYa~LI~~AI~sSP~kk-LTLsEIY~~I~~~fPYyR~~~~gWKNSIRHNLSlN~-----~FvKv~R~~~GKG~~Wtld 173 (395)
.-+|..||..||...-++. ..+.-|+.||..+|+.|.-.. +--|..++|.. .|+.+ .|.|.-|...
T Consensus 44 ~P~~~~mi~eAi~a~keR~GsS~aAikK~i~~~Y~g~~v~k----~n~~lk~alK~~v~~g~l~Qt----kG~GAsGsFk 115 (243)
T KOG4012|consen 44 HPPYSEMITEAISALKERKGSSLAAIKKYIAANYPGDDVEK----NNSRLKLALKKGVSKGVLVQT----KGTGASGSFK 115 (243)
T ss_pred CCcHHHHHHHHHHHhhhcccchHHHHHHHHhhcCccchhhh----hhHHHHHHHHhhhccCceeee----ccCCcccccc
Confidence 3459999999999987766 899999999999998775322 22344445443 33332 3666666554
No 15
>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=70.21 E-value=1.3 Score=34.63 Aligned_cols=58 Identities=16% Similarity=0.247 Sum_probs=37.3
Q ss_pred CCHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCccccCCCCcccccccccc-----ccchhcccC
Q psy723 101 HSYIGLIAMAILSSPEMKLVLSDIYQYILDNYSYFRTRGPGWRNSIRHNLS-----LNDCFIKAG 160 (395)
Q Consensus 101 ySYa~LI~~AI~sSP~kkLTLsEIY~~I~~~fPYyR~~~~gWKNSIRHNLS-----lN~~FvKv~ 160 (395)
+||..++...+.... +.|+.+||++.|.++--| ...++...++|+-.|. .+..|+++.
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 478888888887776 899999999999977544 3336667777874443 345798874
No 16
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=41.17 E-value=22 Score=29.13 Aligned_cols=71 Identities=18% Similarity=0.260 Sum_probs=44.3
Q ss_pred CHHHHHHHHHhc--CCCCCCCHHHHHHHHHhcCCccc------c-CC---CCccccccccccccchhcccCcCCCCCcce
Q psy723 102 SYIGLIAMAILS--SPEMKLVLSDIYQYILDNYSYFR------T-RG---PGWRNSIRHNLSLNDCFIKAGRSANGKGHY 169 (395)
Q Consensus 102 SYa~LI~~AI~s--SP~kkLTLsEIY~~I~~~fPYyR------~-~~---~gWKNSIRHNLSlN~~FvKv~R~~~GKG~~ 169 (395)
+|..|+...|.. .-.+.++.+||++.|.++|..=- . .+ .-|+|.|+=.++--.+.--+.+ +++| +
T Consensus 1 ~~~~~~~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~~~~~~~sg~~~~~~~~ri~Wa~~~L~~aGli~~--~~rG-~ 77 (92)
T PF14338_consen 1 TYDELMPPILEALKDLGGSASRKEIYERVAERFGLSDEERNERLPSGQGYSRFKNRIRWARSYLKKAGLIER--PKRG-I 77 (92)
T ss_pred CHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHhCCCHHHHHHHcccCCcchhHHHhHHHHHHHHHHCCCccC--CCCC-c
Confidence 355666555433 33578999999999999987531 1 12 2588888866654333333332 3344 9
Q ss_pred eeecCC
Q psy723 170 WSIHPA 175 (395)
Q Consensus 170 WtldP~ 175 (395)
|.|.+.
T Consensus 78 ~~iT~~ 83 (92)
T PF14338_consen 78 WRITEK 83 (92)
T ss_pred eEECHh
Confidence 999764
No 17
>PF03373 Octapeptide: Octapeptide repeat; InterPro: IPR005038 This octapeptide repeat is found in several bacterial proteins. The function of this repeat is unknown.; GO: 0019865 immunoglobulin binding
Probab=33.62 E-value=20 Score=18.38 Aligned_cols=8 Identities=75% Similarity=1.290 Sum_probs=5.7
Q ss_pred CCccccCC
Q psy723 329 PGEEDRNK 336 (395)
Q Consensus 329 ~~~~~~~~ 336 (395)
||+||.||
T Consensus 1 PgkeDnnk 8 (8)
T PF03373_consen 1 PGKEDNNK 8 (8)
T ss_pred CccccccC
Confidence 67777765
No 18
>COG2958 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.13 E-value=49 Score=33.60 Aligned_cols=67 Identities=19% Similarity=0.332 Sum_probs=46.0
Q ss_pred CHHHHHHHHHhcCCCCCCCHHHHHHHHHhcCCc------cccCCCCc------cccccccccccchhcccCcCCCCCcce
Q psy723 102 SYIGLIAMAILSSPEMKLVLSDIYQYILDNYSY------FRTRGPGW------RNSIRHNLSLNDCFIKAGRSANGKGHY 169 (395)
Q Consensus 102 SYa~LI~~AI~sSP~kkLTLsEIY~~I~~~fPY------yR~~~~gW------KNSIRHNLSlN~~FvKv~R~~~GKG~~ 169 (395)
+|..+| ++++...+.++|..|||+|+...||- |...+..= --+.|-||-.+--|.||. .|..-|
T Consensus 6 ~~~e~v-l~~Lq~~~ep~t~~eI~eka~e~~~~~~~~kk~~s~g~tp~q~va~~iy~~~~lq~~~pflKvt---e~P~~~ 81 (307)
T COG2958 6 NLIEIV-LSVLQTSEEPFTAREIAEKAFETFPAECQEKKFDSGGDTPQQLVAEIIYTRPNLQEKHPFLKVT---EGPRLY 81 (307)
T ss_pred hhHHHH-HHHHHccCCCCcHHHHHHHHHHhccHHHHHHhhccccccHHHHHHHHHhcCccccccCcccccc---cCceEE
Confidence 456665 45555588899999999999999985 22222222 245677888888999986 346667
Q ss_pred eee
Q psy723 170 WSI 172 (395)
Q Consensus 170 Wtl 172 (395)
|--
T Consensus 82 ~lk 84 (307)
T COG2958 82 YLK 84 (307)
T ss_pred eec
Confidence 753
No 19
>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=24.20 E-value=1.1e+02 Score=25.79 Aligned_cols=33 Identities=9% Similarity=0.144 Sum_probs=28.8
Q ss_pred HHHHHHHHH--hcCCCCCCCHHHHHHHHHhcCCcc
Q psy723 103 YIGLIAMAI--LSSPEMKLVLSDIYQYILDNYSYF 135 (395)
Q Consensus 103 Ya~LI~~AI--~sSP~kkLTLsEIY~~I~~~fPYy 135 (395)
-+..|+.|| +++.....|+..|.+++.++||--
T Consensus 12 L~EvlC~~I~dln~~~~~at~E~l~~~L~~~yp~i 46 (80)
T PF10264_consen 12 LPEVLCWVISDLNAAGQPATQETLREHLRKHYPGI 46 (80)
T ss_pred HHHHHHHHHHHHhccCCcchHHHHHHHHHHhCCCC
Confidence 567888998 568899999999999999999953
No 20
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=23.73 E-value=71 Score=24.41 Aligned_cols=53 Identities=26% Similarity=0.270 Sum_probs=34.9
Q ss_pred HHHHHHHHHhcCC--CCCCCHHHHHHHHHhcCCccccCCCCccccccccc-cccchh
Q psy723 103 YIGLIAMAILSSP--EMKLVLSDIYQYILDNYSYFRTRGPGWRNSIRHNL-SLNDCF 156 (395)
Q Consensus 103 Ya~LI~~AI~sSP--~kkLTLsEIY~~I~~~fPYyR~~~~gWKNSIRHNL-SlN~~F 156 (395)
-..+|..+|.+.. ++.+.|+++-.++..+||-|....=|.. +++.-| ++-+.|
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 4567888885544 3589999999999999988886665554 344444 334444
Done!