Query psy8120
Match_columns 463
No_of_seqs 202 out of 837
Neff 3.4
Searched_HMMs 46136
Date Fri Aug 16 19:07:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8120.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8120hhsearch_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 5.7E-37 1.2E-41 258.8 5.3 96 288-383 1-96 (96)
2 cd00059 FH Forkhead (FH), also 100.0 7.6E-36 1.7E-40 244.5 7.4 78 288-365 1-78 (78)
3 smart00339 FH FORKHEAD. FORKHE 100.0 5.6E-35 1.2E-39 244.0 7.7 88 288-375 1-88 (89)
4 KOG3562|consensus 100.0 8.5E-35 1.8E-39 278.3 7.5 103 281-383 6-108 (277)
5 KOG3563|consensus 100.0 4.4E-35 9.6E-40 294.5 4.9 103 283-385 168-271 (454)
6 KOG2294|consensus 100.0 1.4E-34 3.1E-39 289.4 -0.6 100 284-383 126-228 (454)
7 KOG4385|consensus 100.0 2.3E-30 5E-35 267.3 -0.4 164 199-367 262-442 (581)
8 COG5025 Transcription factor o 99.8 2.4E-21 5.2E-26 206.8 8.9 102 280-381 329-430 (610)
9 COG5025 Transcription factor o 99.5 2.7E-15 5.8E-20 160.9 -0.4 96 284-379 82-177 (610)
10 PF00538 Linker_histone: linke 91.2 0.25 5.4E-06 40.2 3.6 57 293-350 5-65 (77)
11 smart00526 H15 Domain in histo 88.8 0.64 1.4E-05 36.6 4.0 32 292-323 6-38 (66)
12 cd00073 H15 linker histone 1 a 84.8 1.3 2.9E-05 37.0 4.0 56 292-350 6-65 (88)
13 PF05066 HARE-HTH: HB1, ASXL, 71.6 2.7 5.8E-05 33.5 1.8 58 291-350 1-63 (72)
14 KOG4012|consensus 63.7 25 0.00053 35.6 7.1 36 292-327 46-82 (243)
15 PF14338 Mrr_N: Mrr N-terminal 48.9 10 0.00022 31.6 1.5 76 292-372 1-88 (92)
16 COG2958 Uncharacterized protei 33.1 50 0.0011 34.3 3.8 72 292-369 6-89 (307)
17 PF12872 OST-HTH: OST-HTH/LOTU 28.3 66 0.0014 25.1 3.0 56 291-347 4-62 (74)
18 TIGR01376 POMP_repeat Chlamydi 25.3 71 0.0015 21.5 2.3 26 128-154 1-26 (27)
19 KOG0162|consensus 23.3 5.3E+02 0.012 30.8 9.9 6 339-344 1067-1072(1106)
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=5.7e-37 Score=258.85 Aligned_cols=96 Identities=54% Similarity=1.026 Sum_probs=89.3
Q ss_pred CCCCcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCcccccccccceeccCCceEeecccCCCCCCceeEeecCC
Q psy8120 288 KPPYSYVALIAMAINNNEHKRATLAEIYNYIAVKFPYFEKNKKGWQNSIRHNLSLNDCFVKVAKEGAGERKGNYWTLATK 367 (463)
Q Consensus 288 KPPySYaaLIamAI~sSP~krLTLsEIYewI~~~FPYYR~~~kGWQNSIRHNLSLNkcFvKVpR~g~~~GKG~yWtLdP~ 367 (463)
||||||++||+|||+++|+++|||+|||+||+.+||||+.+..+||||||||||+|+||+||++.++..|||+||+|+++
T Consensus 1 KPp~sY~~LI~~Ai~~sp~~~Ltl~eIy~~i~~~~pyyr~~~~~WknSIRHnLS~~~~F~kv~~~~~~~gkg~~W~i~~~ 80 (96)
T PF00250_consen 1 KPPYSYATLIAMAILSSPDKRLTLSEIYEWIEENFPYYRDASKGWKNSIRHNLSLNKCFVKVPRDPSEPGKGSYWTIDPE 80 (96)
T ss_dssp -SSS-HHHHHHHHHHTSTTSEBEHHHHHHHHHHHCGHHHCTHCHHHHHHHHHHHHSTTEEEESCCTSSSSSSEEEEE-CT
T ss_pred CCCCcHHHHHHHHHHhCCCCCccHHHHHHHHHHhhccccccchhhhhHHhhhccccceeeecCcCCCCCCCceeEEeCHH
Confidence 89999999999999999999999999999999999999999999999999999999999999998888899999999999
Q ss_pred hhhhhhccccccccCC
Q psy8120 368 HEDMFENGNYRRRRRM 383 (463)
Q Consensus 368 ~e~~fe~g~~RrRRr~ 383 (463)
+...|+++.+++||++
T Consensus 81 ~~~~~~~~~~~~~~~~ 96 (96)
T PF00250_consen 81 AIEEFEKGRFKRRRKR 96 (96)
T ss_dssp HHHHHHHSCCSSSSSS
T ss_pred HHHHHhcchhhhhhcc
Confidence 9999999988877653
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=7.6e-36 Score=244.52 Aligned_cols=78 Identities=64% Similarity=1.110 Sum_probs=76.4
Q ss_pred CCCCcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCcccccccccceeccCCceEeecccCCCCCCceeEeec
Q psy8120 288 KPPYSYVALIAMAINNNEHKRATLAEIYNYIAVKFPYFEKNKKGWQNSIRHNLSLNDCFVKVAKEGAGERKGNYWTLA 365 (463)
Q Consensus 288 KPPySYaaLIamAI~sSP~krLTLsEIYewI~~~FPYYR~~~kGWQNSIRHNLSLNkcFvKVpR~g~~~GKG~yWtLd 365 (463)
||||||++||++||+++|+++|||+|||+||+++||||+.+.+|||||||||||+|+||+||+|..+++|||+||+||
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 899999999999999999999999999999999999999999999999999999999999999998888999999996
No 3
>smart00339 FH FORKHEAD. FORKHEAD, also known as a "winged helix"
Probab=100.00 E-value=5.6e-35 Score=244.02 Aligned_cols=88 Identities=66% Similarity=1.167 Sum_probs=83.7
Q ss_pred CCCCcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCcccccccccceeccCCceEeecccCCCCCCceeEeecCC
Q psy8120 288 KPPYSYVALIAMAINNNEHKRATLAEIYNYIAVKFPYFEKNKKGWQNSIRHNLSLNDCFVKVAKEGAGERKGNYWTLATK 367 (463)
Q Consensus 288 KPPySYaaLIamAI~sSP~krLTLsEIYewI~~~FPYYR~~~kGWQNSIRHNLSLNkcFvKVpR~g~~~GKG~yWtLdP~ 367 (463)
||||||++||++||+++|+++|||+|||+||+++||||+.+.+|||||||||||+|+||+||+|..+.+|||+||+|+++
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 89999999999999999999999999999999999999999999999999999999999999998877899999999999
Q ss_pred hhhhhhcc
Q psy8120 368 HEDMFENG 375 (463)
Q Consensus 368 ~e~~fe~g 375 (463)
++.+|+.+
T Consensus 81 ~~~~~~~~ 88 (89)
T smart00339 81 AENMFENG 88 (89)
T ss_pred HHHHHhcC
Confidence 98866543
No 4
>KOG3562|consensus
Probab=100.00 E-value=8.5e-35 Score=278.33 Aligned_cols=103 Identities=48% Similarity=0.916 Sum_probs=97.2
Q ss_pred CCCCCCCCCCCcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCcccccccccceeccCCceEeecccCCCCCCce
Q psy8120 281 STTTDSNKPPYSYVALIAMAINNNEHKRATLAEIYNYIAVKFPYFEKNKKGWQNSIRHNLSLNDCFVKVAKEGAGERKGN 360 (463)
Q Consensus 281 ~~~~~~~KPPySYaaLIamAI~sSP~krLTLsEIYewI~~~FPYYR~~~kGWQNSIRHNLSLNkcFvKVpR~g~~~GKG~ 360 (463)
......+||||||+.|.+|||++|++|+|.|+|||+||+++|||||+|++.||||+|||||+|+||+||+|..+.+|||+
T Consensus 6 k~sY~dQKPPYSYIsLTaMAI~~SpekmLPLseIYkfImDrFPfYRkNTQrWQNSLRHNLSFNDCFIKiPRr~drpGKGs 85 (277)
T KOG3562|consen 6 KNSYGDQKPPYSYISLTAMAIQSSPEKMLPLSEIYKFIMDRFPFYRKNTQRWQNSLRHNLSFNDCFIKIPRRPDRPGKGS 85 (277)
T ss_pred cccccccCCCceeeehhhHHhhcChhhcCcHHHHHHHHHhhCchhhhchHHHHHHhhccccccceeeecCCCCCCCCCcc
Confidence 34567899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEeecCChhhhhhccccccccCC
Q psy8120 361 YWTLATKHEDMFENGNYRRRRRM 383 (463)
Q Consensus 361 yWtLdP~~e~~fe~g~~RrRRr~ 383 (463)
||+|+|.+.+|||+|.+.|||++
T Consensus 86 yWalHP~a~dMFENGS~LRRrKR 108 (277)
T KOG3562|consen 86 YWALHPSAFDMFENGSLLRRRKR 108 (277)
T ss_pred ceeeccchhhhcccchHHHHhhh
Confidence 99999999999999998655443
No 5
>KOG3563|consensus
Probab=100.00 E-value=4.4e-35 Score=294.49 Aligned_cols=103 Identities=52% Similarity=0.942 Sum_probs=96.6
Q ss_pred CCCCCCCCCcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCcccccccccceeccCCceEeecccCCCCCCceeE
Q psy8120 283 TTDSNKPPYSYVALIAMAINNNEHKRATLAEIYNYIAVKFPYFEKNKKGWQNSIRHNLSLNDCFVKVAKEGAGERKGNYW 362 (463)
Q Consensus 283 ~~~~~KPPySYaaLIamAI~sSP~krLTLsEIYewI~~~FPYYR~~~kGWQNSIRHNLSLNkcFvKVpR~g~~~GKG~yW 362 (463)
.....||||||+.||.|||+.+|.|+|||+|||+||++.|||||.|.+.|||||||.||+|+|||||+|.++.+|||+||
T Consensus 168 sY~haKPPYSYISLITMAIQ~~pskmLTLSEIYqwIMDLFPyYrqNQQRWQNSIRHSLSFNDCFVKVaRSPDKPGKGSfW 247 (454)
T KOG3563|consen 168 SYTHAKPPYSYISLITMAIQQAPSKMLTLSEIYQWIMDLFPYYRQNQQRWQNSIRHSLSFNDCFVKVARSPDKPGKGSFW 247 (454)
T ss_pred cccCCCCChhHHHHHHHHHHhCCccceeHHHHHHHHHHhhhHhhhhHHHHHhhhhhhccccceeeeccCCCCCCCCccce
Confidence 45678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecCChhhhhhccccccc-cCCCC
Q psy8120 363 TLATKHEDMFENGNYRRR-RRMKR 385 (463)
Q Consensus 363 tLdP~~e~~fe~g~~RrR-Rr~kr 385 (463)
+|+|.+.+|||+|-+.|| ||+|-
T Consensus 248 TLHpdsGNMFENGCYLRRQKRFK~ 271 (454)
T KOG3563|consen 248 TLHPDSGNMFENGCYLRRQKRFKC 271 (454)
T ss_pred eecCCcCcccccchhehhhhhhhh
Confidence 999999999999977554 55543
No 6
>KOG2294|consensus
Probab=99.98 E-value=1.4e-34 Score=289.37 Aligned_cols=100 Identities=58% Similarity=1.023 Sum_probs=95.1
Q ss_pred CCCCCCCCcHHHHHHHHHhcCCCCCcCHHHHHHHHHh-cCCccccCc-ccccccccceeccCCceEeecccCCCCCCcee
Q psy8120 284 TDSNKPPYSYVALIAMAINNNEHKRATLAEIYNYIAV-KFPYFEKNK-KGWQNSIRHNLSLNDCFVKVAKEGAGERKGNY 361 (463)
Q Consensus 284 ~~~~KPPySYaaLIamAI~sSP~krLTLsEIYewI~~-~FPYYR~~~-kGWQNSIRHNLSLNkcFvKVpR~g~~~GKG~y 361 (463)
....||||||++||+|||+.+++|||||+|||+||+. +|||||.+. .|||||||||||||+||+||+|+.+.+|||+|
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 6789999999999999999999999999999999995 999999999 99999999999999999999998888899999
Q ss_pred EeecCChhh-hhhccccccccCC
Q psy8120 362 WTLATKHED-MFENGNYRRRRRM 383 (463)
Q Consensus 362 WtLdP~~e~-~fe~g~~RrRRr~ 383 (463)
|+|+|++++ +|++|.++|||+.
T Consensus 206 W~ldP~~~~~~~~~g~~~rr~~~ 228 (454)
T KOG2294|consen 206 WTLDPDDENNMFDNGSFRRRRRS 228 (454)
T ss_pred cccCcchhccccccccccccccc
Confidence 999999998 9999999877664
No 7
>KOG4385|consensus
Probab=99.95 E-value=2.3e-30 Score=267.33 Aligned_cols=164 Identities=31% Similarity=0.500 Sum_probs=144.5
Q ss_pred CCCceeeEeecCCC-----CCCccccccCccccCCCCCCC-------CCCCCCCCCCCccccCCCCCCCCCCCCCCCCCC
Q psy8120 199 SAGRTTSVIISNSP-----EPKQQILGENSNVQNKKPDPQ-------ENQTTPRNKKTKVSQKNSSSQPSSSSPPPDESS 266 (463)
Q Consensus 199 ~~~r~~~~~~s~~P-----kP~~~~la~~S~~~~~kp~p~-------~~~TSPaqp~tp~sQ~pSss~p~sSSp~ps~~s 266 (463)
++.|++-||++.+. |+..++++.+|.+..++..-+ +++|.++.|+++..+.+++..+++.......++
T Consensus 262 e~erlqamm~hl~~~~s~~k~~~~~~n~vs~~s~~~s~~sss~qs~~~~atgs~gPl~p~~~gp~~~~t~~~pds~p~rr 341 (581)
T KOG4385|consen 262 ESERLQAMMAHLAMKPSEPKASSQPLNLVSSVSFSKSAASSSPQSLPQQATGSTGPLTPATQGPSVITTASAPDSGPARR 341 (581)
T ss_pred HHHHHHHHHHHhhcccCCCccccCCcccccchhhhhhhhhcCCCcccccCCCCCCcccccccCCCccccccCCCccchhh
Confidence 34477888888766 455777888888877665433 788999999999999999999999999999999
Q ss_pred CccccCCCCCCCCCCCC-----CCCCCCCCcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCcccccccccceec
Q psy8120 267 STSIKVSSPISSPSSTT-----TDSNKPPYSYVALIAMAINNNEHKRATLAEIYNYIAVKFPYFEKNKKGWQNSIRHNLS 341 (463)
Q Consensus 267 ~~S~~~s~P~ss~~~~~-----~~~~KPPySYaaLIamAI~sSP~krLTLsEIYewI~~~FPYYR~~~kGWQNSIRHNLS 341 (463)
+.++++..|++++...+ ..+.||||+||.||.+||+++|+|.|||+|||.|+.+.|.|||.|...|||+||||||
T Consensus 342 R~sDk~~~Pisseia~N~dfyk~~dvRPPfTYAsLIRqAIlESpdkQLTLNEIY~WFTrtFAYFRRNaATWKnAVRHNLS 421 (581)
T KOG4385|consen 342 RHSDKYNGPISSEIAQNMDFYKNADVRPPFTYASLIRQAILESPDKQLTLNEIYNWFTRTFAYFRRNAATWKNAVRHNLS 421 (581)
T ss_pred cccccccCchhHHhhhhhhhhhccccCCchhHHHHHHHHHhcCchhhccHHHHHHHHHHHHHHHhccchhHhHHHhhhhH
Confidence 99999999999866554 5678899999999999999999999999999999999999999999999999999999
Q ss_pred cCCceEeecccCCCCCCceeEeecCC
Q psy8120 342 LNDCFVKVAKEGAGERKGNYWTLATK 367 (463)
Q Consensus 342 LNkcFvKVpR~g~~~GKG~yWtLdP~ 367 (463)
|+|||++|+.- ||..|++|..
T Consensus 422 LHKCF~RVEnv-----kgavwtvDe~ 442 (581)
T KOG4385|consen 422 LHKCFVRVENV-----KGAVWTVDER 442 (581)
T ss_pred HHHHHHHHHHH-----hcceeeeehh
Confidence 99999999863 8899999865
No 8
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.84 E-value=2.4e-21 Score=206.81 Aligned_cols=102 Identities=35% Similarity=0.609 Sum_probs=92.7
Q ss_pred CCCCCCCCCCCCcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCcccccccccceeccCCceEeecccCCCCCCc
Q psy8120 280 SSTTTDSNKPPYSYVALIAMAINNNEHKRATLAEIYNYIAVKFPYFEKNKKGWQNSIRHNLSLNDCFVKVAKEGAGERKG 359 (463)
Q Consensus 280 ~~~~~~~~KPPySYaaLIamAI~sSP~krLTLsEIYewI~~~FPYYR~~~kGWQNSIRHNLSLNkcFvKVpR~g~~~GKG 359 (463)
........||+++|+.||.+||+.++.++|+|.+||.||..+|||||....+||||||||||+|+||.||+|...++|||
T Consensus 329 s~~~~~~~kP~~sya~~iT~ail~s~~~kmsls~Iy~~i~s~~pyYr~~p~~w~nSiRhnlSlNksf~kvP~sa~~pGKg 408 (610)
T COG5025 329 SADVNRTSKPAFSYANSITQAILSSPSGKMTLSEIYSWISSNLPYYRHKPTAWQNSIRHNLSLNKSFEKVPRSASQPGKG 408 (610)
T ss_pred ccccccCccCCcchhhhhHHHhhcCcccccccccccccccccchhhccCCcccCchhhhhhhhccccccCCCCcCCCCCc
Confidence 34557788999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeEeecCChhhhhhcccccccc
Q psy8120 360 NYWTLATKHEDMFENGNYRRRR 381 (463)
Q Consensus 360 ~yWtLdP~~e~~fe~g~~RrRR 381 (463)
+||.|+.+....|+....++++
T Consensus 409 ~fw~i~~s~~~~~~sk~~~~s~ 430 (610)
T COG5025 409 CFWKIDYSYIYEKESKRNPRSP 430 (610)
T ss_pred ccCccChhhhhhhcccccccCc
Confidence 9999999988777654444333
No 9
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.49 E-value=2.7e-15 Score=160.91 Aligned_cols=96 Identities=41% Similarity=0.693 Sum_probs=89.2
Q ss_pred CCCCCCCCcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCcccccccccceeccCCceEeecccCCCCCCceeEe
Q psy8120 284 TDSNKPPYSYVALIAMAINNNEHKRATLAEIYNYIAVKFPYFEKNKKGWQNSIRHNLSLNDCFVKVAKEGAGERKGNYWT 363 (463)
Q Consensus 284 ~~~~KPPySYaaLIamAI~sSP~krLTLsEIYewI~~~FPYYR~~~kGWQNSIRHNLSLNkcFvKVpR~g~~~GKG~yWt 363 (463)
....||||+|+.||.++|+++++++|||..||.||...|.||.....+|||+|||||+++++|.|+.+..+..+||+||.
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 34579999999999999999999999999999999999999999999999999999999999999999888889999999
Q ss_pred ecCChhhhhhcccccc
Q psy8120 364 LATKHEDMFENGNYRR 379 (463)
Q Consensus 364 LdP~~e~~fe~g~~Rr 379 (463)
+.|..+..|.....+.
T Consensus 162 igP~~~~~~l~~g~~~ 177 (610)
T COG5025 162 IGPGHETQFLKSGLRL 177 (610)
T ss_pred cCCCccceeecccccc
Confidence 9999998887665544
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=91.22 E-value=0.25 Score=40.17 Aligned_cols=57 Identities=25% Similarity=0.363 Sum_probs=38.7
Q ss_pred HHHHHHHHHhcCCC-CCcCHHHHHHHHHhcCCccccCcccccccccceec---cCCceEeec
Q psy8120 293 YVALIAMAINNNEH-KRATLAEIYNYIAVKFPYFEKNKKGWQNSIRHNLS---LNDCFVKVA 350 (463)
Q Consensus 293 YaaLIamAI~sSP~-krLTLsEIYewI~~~FPYYR~~~kGWQNSIRHNLS---LNkcFvKVp 350 (463)
|..||..||.+..+ +..++..|..||+.+|+.-. ....-+..|+..|- -+..|+++.
T Consensus 5 y~~mI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~-~~~~~~~~l~~aLk~~v~~G~l~~~k 65 (77)
T PF00538_consen 5 YSDMILEAIKALKERKGSSLQAIKKYIKAKYKVDL-NPANFKSRLKRALKRGVEKGKLVQVK 65 (77)
T ss_dssp HHHHHHHHHHHCCSSSSEEHHHHHHHHHHHSSCCC-CHTTHHHHHHHHHHHHHHCTSEEECS
T ss_pred HHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcCcCC-ChHHHHHHHHHHHHHHHHCCcEEeec
Confidence 99999999998544 88999999999999997421 11233444444442 244566554
No 11
>smart00526 H15 Domain in histone families 1 and 5.
Probab=88.85 E-value=0.64 Score=36.59 Aligned_cols=32 Identities=28% Similarity=0.487 Sum_probs=28.2
Q ss_pred cHHHHHHHHHhcCCC-CCcCHHHHHHHHHhcCC
Q psy8120 292 SYVALIAMAINNNEH-KRATLAEIYNYIAVKFP 323 (463)
Q Consensus 292 SYaaLIamAI~sSP~-krLTLsEIYewI~~~FP 323 (463)
+|..||..||....+ +..++..|..||..+|+
T Consensus 6 ~~~~mI~eAI~~l~er~GsS~~aI~kyi~~~~~ 38 (66)
T smart00526 6 PYSEMITEAISALKERKGSSLQAIKKYIEANYK 38 (66)
T ss_pred CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCC
Confidence 699999999998655 66999999999999965
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=84.80 E-value=1.3 Score=37.05 Aligned_cols=56 Identities=23% Similarity=0.414 Sum_probs=38.9
Q ss_pred cHHHHHHHHHhc-CCCCCcCHHHHHHHHHhcCCccccCccccccccccee---ccCCceEeec
Q psy8120 292 SYVALIAMAINN-NEHKRATLAEIYNYIAVKFPYFEKNKKGWQNSIRHNL---SLNDCFVKVA 350 (463)
Q Consensus 292 SYaaLIamAI~s-SP~krLTLsEIYewI~~~FPYYR~~~kGWQNSIRHNL---SLNkcFvKVp 350 (463)
+|..||..||.. .+.+..++..|..||..+|+.-. ..+..-++..| -.+..|+++.
T Consensus 6 ~y~~MI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~---~~~~~~l~~aLkk~v~~G~l~~~k 65 (88)
T cd00073 6 PYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDD---ENFNKLLKLALKKGVAKGKLVQVK 65 (88)
T ss_pred CHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCcch---HHHHHHHHHHHHHHHHCCCeEeec
Confidence 589999999997 46677999999999999987543 33333344443 2244566553
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=71.61 E-value=2.7 Score=33.49 Aligned_cols=58 Identities=22% Similarity=0.271 Sum_probs=38.2
Q ss_pred CcHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCccccCcccccccccceec-----cCCceEeec
Q psy8120 291 YSYVALIAMAINNNEHKRATLAEIYNYIAVKFPYFEKNKKGWQNSIRHNLS-----LNDCFVKVA 350 (463)
Q Consensus 291 ySYaaLIamAI~sSP~krLTLsEIYewI~~~FPYYR~~~kGWQNSIRHNLS-----LNkcFvKVp 350 (463)
+|+..++...|+... +-|+++||++.|++.--| ....+...++|+-.|. .+..|++|.
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 478888888888877 779999999999876543 3346777888873332 455899884
No 14
>KOG4012|consensus
Probab=63.65 E-value=25 Score=35.57 Aligned_cols=36 Identities=36% Similarity=0.510 Sum_probs=31.3
Q ss_pred cHHHHHHHHHhcC-CCCCcCHHHHHHHHHhcCCcccc
Q psy8120 292 SYVALIAMAINNN-EHKRATLAEIYNYIAVKFPYFEK 327 (463)
Q Consensus 292 SYaaLIamAI~sS-P~krLTLsEIYewI~~~FPYYR~ 327 (463)
+|..||..||..+ .....++.-|+.||..+|+.|.-
T Consensus 46 ~~~~mi~eAi~a~keR~GsS~aAikK~i~~~Y~g~~v 82 (243)
T KOG4012|consen 46 PYSEMITEAISALKERKGSSLAAIKKYIAANYPGDDV 82 (243)
T ss_pred cHHHHHHHHHHHhhhcccchHHHHHHHHhhcCccchh
Confidence 4999999999986 55679999999999999988763
No 15
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=48.92 E-value=10 Score=31.62 Aligned_cols=76 Identities=18% Similarity=0.324 Sum_probs=47.9
Q ss_pred cHHHHHHHHHhc--CCCCCcCHHHHHHHHHhcCCccc--------cCc--ccccccccceeccCCceEeecccCCCCCCc
Q psy8120 292 SYVALIAMAINN--NEHKRATLAEIYNYIAVKFPYFE--------KNK--KGWQNSIRHNLSLNDCFVKVAKEGAGERKG 359 (463)
Q Consensus 292 SYaaLIamAI~s--SP~krLTLsEIYewI~~~FPYYR--------~~~--kGWQNSIRHNLSLNkcFvKVpR~g~~~GKG 359 (463)
+|..|+...|.. .-.+.++.+||++.|.++|..=. ... .-|+|.|+=.++--++.--|.+. .+
T Consensus 1 ~~~~~~~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~~~~~~~sg~~~~~~~~ri~Wa~~~L~~aGli~~~----~r- 75 (92)
T PF14338_consen 1 TYDELMPPILEALKDLGGSASRKEIYERVAERFGLSDEERNERLPSGQGYSRFKNRIRWARSYLKKAGLIERP----KR- 75 (92)
T ss_pred CHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHhCCCHHHHHHHcccCCcchhHHHhHHHHHHHHHHCCCccCC----CC-
Confidence 355666555443 33588999999999999997431 111 25999998666544433333332 13
Q ss_pred eeEeecCChhhhh
Q psy8120 360 NYWTLATKHEDMF 372 (463)
Q Consensus 360 ~yWtLdP~~e~~f 372 (463)
.+|.|.+.....+
T Consensus 76 G~~~iT~~G~~~l 88 (92)
T PF14338_consen 76 GIWRITEKGRKAL 88 (92)
T ss_pred CceEECHhHHHHH
Confidence 3899998765443
No 16
>COG2958 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.13 E-value=50 Score=34.28 Aligned_cols=72 Identities=18% Similarity=0.194 Sum_probs=47.7
Q ss_pred cHHHHHHHHHhcCCCCCcCHHHHHHHHHhcCCcc------ccCcc------cccccccceeccCCceEeecccCCCCCCc
Q psy8120 292 SYVALIAMAINNNEHKRATLAEIYNYIAVKFPYF------EKNKK------GWQNSIRHNLSLNDCFVKVAKEGAGERKG 359 (463)
Q Consensus 292 SYaaLIamAI~sSP~krLTLsEIYewI~~~FPYY------R~~~k------GWQNSIRHNLSLNkcFvKVpR~g~~~GKG 359 (463)
+|..+|-..++. .+..+|..|||+|+.+.||-= ...++ +=--+.|-||-.+--|.||... ..
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 466666555555 777899999999999999842 22222 1224567788888899998643 23
Q ss_pred eeEeecCChh
Q psy8120 360 NYWTLATKHE 369 (463)
Q Consensus 360 ~yWtLdP~~e 369 (463)
-||--..+.+
T Consensus 80 ~~~lke~~~e 89 (307)
T COG2958 80 LYYLKEAADE 89 (307)
T ss_pred EEeeccccch
Confidence 4665544433
No 17
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=28.30 E-value=66 Score=25.05 Aligned_cols=56 Identities=20% Similarity=0.303 Sum_probs=35.8
Q ss_pred CcHHHHHHHHHhcCC--CCCcCHHHHHHHHHhcCCccccCccccccccccee-ccCCceE
Q psy8120 291 YSYVALIAMAINNNE--HKRATLAEIYNYIAVKFPYFEKNKKGWQNSIRHNL-SLNDCFV 347 (463)
Q Consensus 291 ySYaaLIamAI~sSP--~krLTLsEIYewI~~~FPYYR~~~kGWQNSIRHNL-SLNkcFv 347 (463)
-.-..+|..+|.+.. ++.+.|+++-.++.++||-|....=|.. +++.=| ++-+.|+
T Consensus 4 ~~~~~~l~~ll~~~~~~~g~v~ls~l~~~~~~~~~~f~~~~yG~~-~l~~ll~~~~~~~~ 62 (74)
T PF12872_consen 4 EELKKLLRELLESQKGEDGWVSLSQLGQEYKKKYPDFDPRDYGFS-SLSELLESLPDVVE 62 (74)
T ss_dssp HHHHHHHHHHHHHTCTTTSSEEHHHHHHHHHHHHTT--TCCTTSS-SHHHHHHT-TTTEE
T ss_pred HHHHHHHHHHHHhCcCCCceEEHHHHHHHHHHHCCCCCccccCCC-cHHHHHHhCCCeEE
Confidence 345678888995544 3579999999999999988875444432 344444 4455554
No 18
>TIGR01376 POMP_repeat Chlamydial polymorphic outer membrane protein repeat. This repeat is observed, but is very rare, outside the Chlamydias.
Probab=25.27 E-value=71 Score=21.49 Aligned_cols=26 Identities=27% Similarity=0.489 Sum_probs=21.8
Q ss_pred CCCCcccccCCCCCCcceEeeeeeeec
Q psy8120 128 RSKPETFHSKDDPGYGSVIYETMTVPL 154 (463)
Q Consensus 128 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 154 (463)
+.++..|..|.....|-.||+. ++.|
T Consensus 1 n~~~i~F~~N~a~~~GGAI~~~-~~~i 26 (27)
T TIGR01376 1 NNGTILFSSNSAKGSGGAIYAT-KISI 26 (27)
T ss_pred CCceEEEecCccCCcccEEEEe-eEEE
Confidence 3567889999999999999998 7766
No 19
>KOG0162|consensus
Probab=23.34 E-value=5.3e+02 Score=30.84 Aligned_cols=6 Identities=33% Similarity=0.578 Sum_probs=3.1
Q ss_pred eeccCC
Q psy8120 339 NLSLND 344 (463)
Q Consensus 339 NLSLNk 344 (463)
-|++++
T Consensus 1067 Els~~~ 1072 (1106)
T KOG0162|consen 1067 ELSFKK 1072 (1106)
T ss_pred cccccC
Confidence 355554
Done!