Query psy12666
Match_columns 347
No_of_seqs 257 out of 794
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 16:23:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12666.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12666hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00059 FH Forkhead (FH), also 100.0 3.8E-31 8.2E-36 210.5 3.2 71 51-132 1-78 (78)
2 PF00250 Fork_head: Fork head 100.0 6.4E-31 1.4E-35 215.9 -0.1 76 51-137 1-83 (96)
3 KOG3563|consensus 100.0 3.8E-30 8.3E-35 251.6 4.0 101 46-166 168-275 (454)
4 smart00339 FH FORKHEAD. FORKHE 100.0 2.1E-29 4.5E-34 204.6 3.1 76 51-137 1-83 (89)
5 KOG2294|consensus 99.9 3.4E-28 7.4E-33 238.8 1.1 80 47-137 126-214 (454)
6 KOG3562|consensus 99.9 5.8E-28 1.3E-32 224.5 1.5 98 47-164 9-113 (277)
7 KOG4385|consensus 99.8 5.7E-20 1.2E-24 185.5 -0.5 77 47-137 364-445 (581)
8 COG5025 Transcription factor o 99.6 8.6E-17 1.9E-21 167.7 5.0 87 43-140 329-422 (610)
9 COG5025 Transcription factor o 99.1 9.4E-12 2E-16 130.4 1.0 80 46-136 81-167 (610)
10 cd06649 PKc_MEK2 Catalytic dom 70.3 2.7 5.9E-05 39.7 1.9 52 56-115 277-328 (331)
11 KOG2236|consensus 68.2 31 0.00067 36.6 9.1 14 82-95 247-266 (483)
12 PF05066 HARE-HTH: HB1, ASXL, 58.2 2.3 5E-05 32.7 -0.9 53 54-118 1-62 (72)
13 smart00526 H15 Domain in histo 50.5 9.1 0.0002 29.0 1.3 27 55-88 6-32 (66)
14 PF00538 Linker_histone: linke 49.3 3.8 8.3E-05 32.1 -0.9 30 55-93 4-33 (77)
15 PF06044 DRP: Dam-replacing fa 32.3 21 0.00045 35.1 0.9 49 55-111 187-236 (254)
16 cd00073 H15 linker histone 1 a 26.4 35 0.00075 27.5 1.2 27 55-88 6-32 (88)
17 PF05265 DUF723: Protein of un 20.8 35 0.00076 26.7 0.2 13 275-287 34-46 (60)
No 1
>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=99.96 E-value=3.8e-31 Score=210.52 Aligned_cols=71 Identities=34% Similarity=0.551 Sum_probs=68.5
Q ss_pred CCcchHHHHHHHHHHhCCCCCCCCCCCCcccccccCCc-----cccccccCCCCchhhhhhhhhcccccccccccc--CC
Q psy12666 51 NDNFFVNKLIVKCQIVNPYLDSSKAFDKPCHMHELWPG-----PLLEIKFRPANHYQNSIRHNLSLHSKFMRVQNE--GT 123 (347)
Q Consensus 51 KPpySYa~LI~~AI~ssP~~~~~~~~~k~LTL~EIY~~-----PYfk~k~~~~~GWKNSIRHNLSLn~~F~Kv~r~--~~ 123 (347)
||||||++||++||+++|+ ++|||+|||+| |||+. +..|||||||||||+|+||+||+|+ +.
T Consensus 1 kP~~sY~~LI~~Ai~~sp~--------~~lTL~eIy~~I~~~~pyyr~---~~~gWknSIRHnLS~n~~F~kv~r~~~~~ 69 (78)
T cd00059 1 KPPYSYSALIAMAIQSSPE--------KRLTLSEIYKWISDNFPYFRD---APAGWQNSIRHNLSLNKCFVKVPREPDEP 69 (78)
T ss_pred CCCCCHHHHHHHHHHhCCC--------CCeeHHHHHHHHHHhCCcccc---CCCCCccceeEecccccceEECCCCCCCC
Confidence 8999999999999999999 99999999999 99998 7899999999999999999999998 78
Q ss_pred CccceeEeC
Q psy12666 124 GKSSWWMLN 132 (347)
Q Consensus 124 GKG~~W~l~ 132 (347)
|||+||+||
T Consensus 70 gkg~~W~i~ 78 (78)
T cd00059 70 GKGSYWTLD 78 (78)
T ss_pred CCCCeeeeC
Confidence 999999986
No 2
>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=99.96 E-value=6.4e-31 Score=215.95 Aligned_cols=76 Identities=30% Similarity=0.553 Sum_probs=69.0
Q ss_pred CCcchHHHHHHHHHHhCCCCCCCCCCCCcccccccCCc-----cccccccCCCCchhhhhhhhhccccccccccc--cCC
Q psy12666 51 NDNFFVNKLIVKCQIVNPYLDSSKAFDKPCHMHELWPG-----PLLEIKFRPANHYQNSIRHNLSLHSKFMRVQN--EGT 123 (347)
Q Consensus 51 KPpySYa~LI~~AI~ssP~~~~~~~~~k~LTL~EIY~~-----PYfk~k~~~~~GWKNSIRHNLSLn~~F~Kv~r--~~~ 123 (347)
||||||+.||++||+++|+ ++|||+|||+| |||+. +..|||||||||||+|+||+||++ +..
T Consensus 1 KPp~sY~~LI~~Ai~~sp~--------~~Ltl~eIy~~i~~~~pyyr~---~~~~WknSIRHnLS~~~~F~kv~~~~~~~ 69 (96)
T PF00250_consen 1 KPPYSYATLIAMAILSSPD--------KRLTLSEIYEWIEENFPYYRD---ASKGWKNSIRHNLSLNKCFVKVPRDPSEP 69 (96)
T ss_dssp -SSS-HHHHHHHHHHTSTT--------SEBEHHHHHHHHHHHCGHHHC---THCHHHHHHHHHHHHSTTEEEESCCTSSS
T ss_pred CCCCcHHHHHHHHHHhCCC--------CCccHHHHHHHHHHhhccccc---cchhhhhHHhhhccccceeeecCcCCCCC
Confidence 8999999999999999999 99999999999 99998 778999999999999999999999 367
Q ss_pred CccceeEeCCCccc
Q psy12666 124 GKSSWWMLNPDAKA 137 (347)
Q Consensus 124 GKG~~W~l~p~~~~ 137 (347)
|||+||+|+++...
T Consensus 70 gkg~~W~i~~~~~~ 83 (96)
T PF00250_consen 70 GKGSYWTIDPEAIE 83 (96)
T ss_dssp SSSEEEEE-CTHHH
T ss_pred CCceeEEeCHHHHH
Confidence 99999999999764
No 3
>KOG3563|consensus
Probab=99.96 E-value=3.8e-30 Score=251.62 Aligned_cols=101 Identities=27% Similarity=0.427 Sum_probs=93.2
Q ss_pred CCCCCCCcchHHHHHHHHHHhCCCCCCCCCCCCcccccccCCc-----cccccccCCCCchhhhhhhhhccccccccccc
Q psy12666 46 VDHFENDNFFVNKLIVKCQIVNPYLDSSKAFDKPCHMHELWPG-----PLLEIKFRPANHYQNSIRHNLSLHSKFMRVQN 120 (347)
Q Consensus 46 ~~~~~KPpySYa~LI~~AI~ssP~~~~~~~~~k~LTL~EIY~~-----PYfk~k~~~~~GWKNSIRHNLSLn~~F~Kv~r 120 (347)
.-...||||||+.||+|||+.+|. |+|||.|||+| |||+. +.+.|||||||.||+|+||+||+|
T Consensus 168 sY~haKPPYSYISLITMAIQ~~ps--------kmLTLSEIYqwIMDLFPyYrq---NQQRWQNSIRHSLSFNDCFVKVaR 236 (454)
T KOG3563|consen 168 SYTHAKPPYSYISLITMAIQQAPS--------KMLTLSEIYQWIMDLFPYYRQ---NQQRWQNSIRHSLSFNDCFVKVAR 236 (454)
T ss_pred cccCCCCChhHHHHHHHHHHhCCc--------cceeHHHHHHHHHHhhhHhhh---hHHHHHhhhhhhccccceeeeccC
Confidence 345789999999999999999999 99999999999 99999 889999999999999999999999
Q ss_pred c--CCCccceeEeCCCccccchhhhhcccccchhhhhhhhhhhhhHhh
Q psy12666 121 E--GTGKSSWWMLNPDAKAGKSARRRATSMETSKFEKRRGRVKKKVEA 166 (347)
Q Consensus 121 ~--~~GKG~~W~l~p~~~~gk~~RRR~~s~~~~k~~Krr~R~kkk~~~ 166 (347)
. .+|||+||+|+|++.. ++|++-+.||+||+|-.+..
T Consensus 237 SPDKPGKGSfWTLHpdsGN---------MFENGCYLRRQKRFK~ekk~ 275 (454)
T KOG3563|consen 237 SPDKPGKGSFWTLHPDSGN---------MFENGCYLRRQKRFKCEKKE 275 (454)
T ss_pred CCCCCCCccceeecCCcCc---------ccccchhehhhhhhhhhhhh
Confidence 6 7899999999999987 89999999999998876543
No 4
>smart00339 FH FORKHEAD. FORKHEAD, also known as a "winged helix"
Probab=99.95 E-value=2.1e-29 Score=204.61 Aligned_cols=76 Identities=36% Similarity=0.575 Sum_probs=71.7
Q ss_pred CCcchHHHHHHHHHHhCCCCCCCCCCCCcccccccCCc-----cccccccCCCCchhhhhhhhhcccccccccccc--CC
Q psy12666 51 NDNFFVNKLIVKCQIVNPYLDSSKAFDKPCHMHELWPG-----PLLEIKFRPANHYQNSIRHNLSLHSKFMRVQNE--GT 123 (347)
Q Consensus 51 KPpySYa~LI~~AI~ssP~~~~~~~~~k~LTL~EIY~~-----PYfk~k~~~~~GWKNSIRHNLSLn~~F~Kv~r~--~~ 123 (347)
||||||+.||++||+++|+ ++|||+|||+| |||+. +..|||||||||||+|+||+|++++ ..
T Consensus 1 kP~~sY~~lI~~ai~~sp~--------~~ltl~~Iy~~I~~~~pyy~~---~~~~WknSIRHnLS~n~~F~kv~~~~~~~ 69 (89)
T smart00339 1 KPPYSYIALIAMAILSSPD--------KRLTLSEIYKWIEDNFPYYRE---NRAGWQNSIRHNLSLNDCFVKVPREGDRP 69 (89)
T ss_pred CCCCCHHHHHHHHHHhCCC--------CCeeHHHHHHHHHHhCchhhc---CccccccccccccchhhceeecCcCCCCC
Confidence 8999999999999999999 99999999999 99998 7779999999999999999999985 45
Q ss_pred CccceeEeCCCccc
Q psy12666 124 GKSSWWMLNPDAKA 137 (347)
Q Consensus 124 GKG~~W~l~p~~~~ 137 (347)
|||+||+|+++++.
T Consensus 70 gkg~~W~i~~~~~~ 83 (89)
T smart00339 70 GKGSYWTLDPDAEN 83 (89)
T ss_pred CCCCEEEECccHHH
Confidence 99999999999875
No 5
>KOG2294|consensus
Probab=99.94 E-value=3.4e-28 Score=238.75 Aligned_cols=80 Identities=29% Similarity=0.451 Sum_probs=74.7
Q ss_pred CCCCCCcchHHHHHHHHHHhCCCCCCCCCCCCcccccccCCc------cccccccCCC-Cchhhhhhhhhcccccccccc
Q psy12666 47 DHFENDNFFVNKLIVKCQIVNPYLDSSKAFDKPCHMHELWPG------PLLEIKFRPA-NHYQNSIRHNLSLHSKFMRVQ 119 (347)
Q Consensus 47 ~~~~KPpySYa~LI~~AI~ssP~~~~~~~~~k~LTL~EIY~~------PYfk~k~~~~-~GWKNSIRHNLSLn~~F~Kv~ 119 (347)
....||||||+.||+|||+.+|+ |+|||.|||+| |||+. .. .|||||||||||||+||+||+
T Consensus 126 ~~~~kpp~SY~~LI~mAI~~Sp~--------krLtLs~Iy~~i~~~~fpyyr~---~~~~gWqNSIRHNLSLn~cF~Kvp 194 (454)
T KOG2294|consen 126 GAGVKPPYSYSGLIAMAIRLSPG--------KRLTLGGIYFYILLEHFPYYRD---ANMPGWKNSIRHNLSLNKCFVKVP 194 (454)
T ss_pred CCCcCCccccccccccccccCCC--------cceeecCeeEEEEecccccccc---CCCccchhhcccccccccCccccC
Confidence 55799999999999999999999 99999999998 99999 66 899999999999999999999
Q ss_pred cc--CCCccceeEeCCCccc
Q psy12666 120 NE--GTGKSSWWMLNPDAKA 137 (347)
Q Consensus 120 r~--~~GKG~~W~l~p~~~~ 137 (347)
|+ ..|||+||+|+++.+.
T Consensus 195 r~~~~~gKg~~W~ldP~~~~ 214 (454)
T KOG2294|consen 195 RERGRPGKGNYWTLDPDDEN 214 (454)
T ss_pred CcccCCCCCCccccCcchhc
Confidence 97 4599999999999775
No 6
>KOG3562|consensus
Probab=99.94 E-value=5.8e-28 Score=224.53 Aligned_cols=98 Identities=26% Similarity=0.409 Sum_probs=92.0
Q ss_pred CCCCCCcchHHHHHHHHHHhCCCCCCCCCCCCcccccccCCc-----cccccccCCCCchhhhhhhhhcccccccccccc
Q psy12666 47 DHFENDNFFVNKLIVKCQIVNPYLDSSKAFDKPCHMHELWPG-----PLLEIKFRPANHYQNSIRHNLSLHSKFMRVQNE 121 (347)
Q Consensus 47 ~~~~KPpySYa~LI~~AI~ssP~~~~~~~~~k~LTL~EIY~~-----PYfk~k~~~~~GWKNSIRHNLSLn~~F~Kv~r~ 121 (347)
-..+||||||+.|-+|||++||+ |+|.|.|||+| ||||. +.+.||||+|||||+|+||+||+|.
T Consensus 9 Y~dQKPPYSYIsLTaMAI~~Spe--------kmLPLseIYkfImDrFPfYRk---NTQrWQNSLRHNLSFNDCFIKiPRr 77 (277)
T KOG3562|consen 9 YGDQKPPYSYISLTAMAIQSSPE--------KMLPLSEIYKFIMDRFPFYRK---NTQRWQNSLRHNLSFNDCFIKIPRR 77 (277)
T ss_pred ccccCCCceeeehhhHHhhcChh--------hcCcHHHHHHHHHhhCchhhh---chHHHHHHhhccccccceeeecCCC
Confidence 35689999999999999999999 99999999998 99999 8899999999999999999999996
Q ss_pred --CCCccceeEeCCCccccchhhhhcccccchhhhhhhhhhhhhH
Q psy12666 122 --GTGKSSWWMLNPDAKAGKSARRRATSMETSKFEKRRGRVKKKV 164 (347)
Q Consensus 122 --~~GKG~~W~l~p~~~~gk~~RRR~~s~~~~k~~Krr~R~kkk~ 164 (347)
..|||+||.|+|.+.. ++|++.+.|||+|++.++
T Consensus 78 ~drpGKGsyWalHP~a~d---------MFENGS~LRRrKRFrv~k 113 (277)
T KOG3562|consen 78 PDRPGKGSYWALHPSAFD---------MFENGSLLRRRKRFRVLK 113 (277)
T ss_pred CCCCCCccceeeccchhh---------hcccchHHHHhhhhhhcc
Confidence 7899999999999986 899999999999988776
No 7
>KOG4385|consensus
Probab=99.76 E-value=5.7e-20 Score=185.47 Aligned_cols=77 Identities=27% Similarity=0.424 Sum_probs=70.7
Q ss_pred CCCCCCcchHHHHHHHHHHhCCCCCCCCCCCCcccccccCCc-----cccccccCCCCchhhhhhhhhcccccccccccc
Q psy12666 47 DHFENDNFFVNKLIVKCQIVNPYLDSSKAFDKPCHMHELWPG-----PLLEIKFRPANHYQNSIRHNLSLHSKFMRVQNE 121 (347)
Q Consensus 47 ~~~~KPpySYa~LI~~AI~ssP~~~~~~~~~k~LTL~EIY~~-----PYfk~k~~~~~GWKNSIRHNLSLn~~F~Kv~r~ 121 (347)
....+|||+|+.||++||+++|+ +.|||+|||.| -|||. +.+.|||+||||||||+||+||.+
T Consensus 364 ~~dvRPPfTYAsLIRqAIlESpd--------kQLTLNEIY~WFTrtFAYFRR---NaATWKnAVRHNLSLHKCF~RVEn- 431 (581)
T KOG4385|consen 364 NADVRPPFTYASLIRQAILESPD--------KQLTLNEIYNWFTRTFAYFRR---NAATWKNAVRHNLSLHKCFVRVEN- 431 (581)
T ss_pred ccccCCchhHHHHHHHHHhcCch--------hhccHHHHHHHHHHHHHHHhc---cchhHhHHHhhhhHHHHHHHHHHH-
Confidence 45689999999999999999999 99999999999 88888 899999999999999999999966
Q ss_pred CCCccceeEeCCCccc
Q psy12666 122 GTGKSSWWMLNPDAKA 137 (347)
Q Consensus 122 ~~GKG~~W~l~p~~~~ 137 (347)
-||.-|++|.-...
T Consensus 432 --vkgavwtvDe~e~~ 445 (581)
T KOG4385|consen 432 --VKGAVWTVDEREFQ 445 (581)
T ss_pred --Hhcceeeeehhhhh
Confidence 59999999876553
No 8
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.64 E-value=8.6e-17 Score=167.68 Aligned_cols=87 Identities=25% Similarity=0.424 Sum_probs=79.9
Q ss_pred CCCCCCCCCCcchHHHHHHHHHHhCCCCCCCCCCCCcccccccCCc-----cccccccCCCCchhhhhhhhhcccccccc
Q psy12666 43 PTQVDHFENDNFFVNKLIVKCQIVNPYLDSSKAFDKPCHMHELWPG-----PLLEIKFRPANHYQNSIRHNLSLHSKFMR 117 (347)
Q Consensus 43 ~~~~~~~~KPpySYa~LI~~AI~ssP~~~~~~~~~k~LTL~EIY~~-----PYfk~k~~~~~GWKNSIRHNLSLn~~F~K 117 (347)
..+.+...||+++|+.||+.||+.+|. ++|+|.+||.| |||+. ...+|+||||||||||++|.|
T Consensus 329 s~~~~~~~kP~~sya~~iT~ail~s~~--------~kmsls~Iy~~i~s~~pyYr~---~p~~w~nSiRhnlSlNksf~k 397 (610)
T COG5025 329 SADVNRTSKPAFSYANSITQAILSSPS--------GKMTLSEIYSWISSNLPYYRH---KPTAWQNSIRHNLSLNKSFEK 397 (610)
T ss_pred ccccccCccCCcchhhhhHHHhhcCcc--------cccccccccccccccchhhcc---CCcccCchhhhhhhhcccccc
Confidence 456778899999999999999999999 88999999999 99999 888999999999999999999
Q ss_pred cccc--CCCccceeEeCCCccccch
Q psy12666 118 VQNE--GTGKSSWWMLNPDAKAGKS 140 (347)
Q Consensus 118 v~r~--~~GKG~~W~l~p~~~~gk~ 140 (347)
|++. ..|||+||.++.+....+.
T Consensus 398 vP~sa~~pGKg~fw~i~~s~~~~~~ 422 (610)
T COG5025 398 VPRSASQPGKGCFWKIDYSYIYEKE 422 (610)
T ss_pred CCCCcCCCCCcccCccChhhhhhhc
Confidence 9997 7899999999999765443
No 9
>COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]
Probab=99.14 E-value=9.4e-12 Score=130.39 Aligned_cols=80 Identities=21% Similarity=0.348 Sum_probs=71.3
Q ss_pred CCCCCCCcchHHHHHHHHHHhCCCCCCCCCCCCcccccccCCc-----cccccccCCCCchhhhhhhhhccccccccccc
Q psy12666 46 VDHFENDNFFVNKLIVKCQIVNPYLDSSKAFDKPCHMHELWPG-----PLLEIKFRPANHYQNSIRHNLSLHSKFMRVQN 120 (347)
Q Consensus 46 ~~~~~KPpySYa~LI~~AI~ssP~~~~~~~~~k~LTL~EIY~~-----PYfk~k~~~~~GWKNSIRHNLSLn~~F~Kv~r 120 (347)
.+.+.||+|+|+.+|.++|+.+++ +++||..||.| .||.- ...+|+|||||||++++.|.++..
T Consensus 81 ~~t~~v~~~s~a~gr~~~il~s~~--------~~lt~s~~~~~~~~~~~~~~k---~~~~~~~sIr~Nls~~~a~~~i~g 149 (610)
T COG5025 81 NWTYYVPPYSYATGRGLAILNSPD--------KPLTLSKIYTWIHNTFFYYAK---VVSRWQNSIRHNLSLNDAFIKIEG 149 (610)
T ss_pred CcccccCCeeeeeccccccccCcc--------cCCcccceeeeeeeccccccc---ccchhhhhhhcccccCceEEEEec
Confidence 445689999999999999999999 99999999999 55555 567999999999999999999987
Q ss_pred c--CCCccceeEeCCCcc
Q psy12666 121 E--GTGKSSWWMLNPDAK 136 (347)
Q Consensus 121 ~--~~GKG~~W~l~p~~~ 136 (347)
. ..+||.||.+.|+.+
T Consensus 150 ~~g~~~~g~~~~igP~~~ 167 (610)
T COG5025 150 RNGAKVKGHFWSIGPGHE 167 (610)
T ss_pred cCCccccceeeccCCCcc
Confidence 6 458999999999765
No 10
>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=70.32 E-value=2.7 Score=39.65 Aligned_cols=52 Identities=15% Similarity=0.245 Sum_probs=45.1
Q ss_pred HHHHHHHHHHhCCCCCCCCCCCCcccccccCCccccccccCCCCchhhhhhhhhcccccc
Q psy12666 56 VNKLIVKCQIVNPYLDSSKAFDKPCHMHELWPGPLLEIKFRPANHYQNSIRHNLSLHSKF 115 (347)
Q Consensus 56 Ya~LI~~AI~ssP~~~~~~~~~k~LTL~EIY~~PYfk~k~~~~~GWKNSIRHNLSLn~~F 115 (347)
+..||..++.-.|+ +|.|+.||.+.|||+......-+|++.+..+|+++.-+
T Consensus 277 l~~li~~~L~~~P~--------~Rpt~~ell~h~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 (331)
T cd06649 277 FQEFVNKCLIKNPA--------ERADLKMLMNHTFIKRSEVEEVDFAGWLCKTLRLNQPS 328 (331)
T ss_pred HHHHHHHHccCCcc--------cCCCHHHHhcChHHhhcccccccHHHHHHHhhcccccc
Confidence 68999999999999 99999999999999875545678999999999987543
No 11
>KOG2236|consensus
Probab=68.20 E-value=31 Score=36.57 Aligned_cols=14 Identities=14% Similarity=0.548 Sum_probs=9.6
Q ss_pred ccccCCc------ccccccc
Q psy12666 82 MHELWPG------PLLEIKF 95 (347)
Q Consensus 82 L~EIY~~------PYfk~k~ 95 (347)
|-+||+- |||.-+|
T Consensus 247 lG~I~EiFGpV~~P~YvvRF 266 (483)
T KOG2236|consen 247 LGQIFEIFGPVKNPYYVVRF 266 (483)
T ss_pred chhhhhhhcccCCceEEEec
Confidence 3455554 9999876
No 12
>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=58.18 E-value=2.3 Score=32.69 Aligned_cols=53 Identities=17% Similarity=0.320 Sum_probs=32.1
Q ss_pred chHHHHHHHHHHhCCCCCCCCCCCCcccccccCCc----cccccccCCCCchhhhhhhhhcc-----ccccccc
Q psy12666 54 FFVNKLIVKCQIVNPYLDSSKAFDKPCHMHELWPG----PLLEIKFRPANHYQNSIRHNLSL-----HSKFMRV 118 (347)
Q Consensus 54 ySYa~LI~~AI~ssP~~~~~~~~~k~LTL~EIY~~----PYfk~k~~~~~GWKNSIRHNLSL-----n~~F~Kv 118 (347)
+||..++.+.|... ++.|+.+|||+. -+|.. ..+...++|+-.|.- +..|+++
T Consensus 1 mt~~eaa~~vL~~~---------~~pm~~~eI~~~i~~~~~~~~---~~k~p~~~i~a~ly~~~~~~d~~F~~v 62 (72)
T PF05066_consen 1 MTFKEAAYEVLEEA---------GRPMTFKEIWEEIQERGLYKK---SGKTPEATIAAQLYTDIKNEDSRFVKV 62 (72)
T ss_dssp S-HHHHHHHHHHHH----------S-EEHHHHHHHHHHHHTS------GGGGGHHHH-HHHHHHH-T-SS-EES
T ss_pred CCHHHHHHHHHHhc---------CCCcCHHHHHHHHHHhCCCCc---ccCCHHHHHHHHHHHHcccCCCCEEEe
Confidence 47888888888543 378999999985 44443 355677888744443 4589998
No 13
>smart00526 H15 Domain in histone families 1 and 5.
Probab=50.46 E-value=9.1 Score=28.98 Aligned_cols=27 Identities=7% Similarity=-0.050 Sum_probs=22.9
Q ss_pred hHHHHHHHHHHhCCCCCCCCCCCCcccccccCCc
Q psy12666 55 FVNKLIVKCQIVNPYLDSSKAFDKPCHMHELWPG 88 (347)
Q Consensus 55 SYa~LI~~AI~ssP~~~~~~~~~k~LTL~EIY~~ 88 (347)
+|..||.+||....+ ++..++..|..|
T Consensus 6 ~~~~mI~eAI~~l~e-------r~GsS~~aI~ky 32 (66)
T smart00526 6 PYSEMITEAISALKE-------RKGSSLQAIKKY 32 (66)
T ss_pred CHHHHHHHHHHHcCC-------CCCCCHHHHHHH
Confidence 689999999988766 467899999984
No 14
>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=49.27 E-value=3.8 Score=32.11 Aligned_cols=30 Identities=7% Similarity=0.043 Sum_probs=24.2
Q ss_pred hHHHHHHHHHHhCCCCCCCCCCCCcccccccCCcccccc
Q psy12666 55 FVNKLIVKCQIVNPYLDSSKAFDKPCHMHELWPGPLLEI 93 (347)
Q Consensus 55 SYa~LI~~AI~ssP~~~~~~~~~k~LTL~EIY~~PYfk~ 93 (347)
+|..||.+||.+.-+ .+..++..|.. |-+.
T Consensus 4 ~y~~mI~eAI~~l~e-------r~GsS~~aI~k--yI~~ 33 (77)
T PF00538_consen 4 PYSDMILEAIKALKE-------RKGSSLQAIKK--YIKA 33 (77)
T ss_dssp CHHHHHHHHHHHCCS-------SSSEEHHHHHH--HHHH
T ss_pred CHHHHHHHHHHHcCC-------CCCCCHHHHHH--HHHH
Confidence 489999999988666 37799999999 4444
No 15
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=32.28 E-value=21 Score=35.05 Aligned_cols=49 Identities=24% Similarity=0.316 Sum_probs=39.2
Q ss_pred hHHHHHHHHHHhCCCCCCCCCCCCcccccccCCc-cccccccCCCCchhhhhhhhhcc
Q psy12666 55 FVNKLIVKCQIVNPYLDSSKAFDKPCHMHELWPG-PLLEIKFRPANHYQNSIRHNLSL 111 (347)
Q Consensus 55 SYa~LI~~AI~ssP~~~~~~~~~k~LTL~EIY~~-PYfk~k~~~~~GWKNSIRHNLSL 111 (347)
.+...|..+|..-+. ...||+|||.| ++++.++.....=+..||..|=.
T Consensus 187 GWlldi~~cid~i~~--------~~FtL~diY~Fe~~L~~~~P~N~~Ik~KIRQqLQ~ 236 (254)
T PF06044_consen 187 GWLLDIMKCIDKIPK--------NEFTLDDIYAFEDELQIKYPNNNHIKAKIRQQLQI 236 (254)
T ss_dssp HHHHHHHHHHHHS-S--------SEEEHHHHHTTHHHHHHHSTT-S-HHHHHHHHHHH
T ss_pred chHHHHHHHHHhcCc--------cceeHHHHHHHHHHHHHhCCCCCChhHHHHHHHHH
Confidence 467788889988777 88999999998 88888887778899999999865
No 16
>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=26.36 E-value=35 Score=27.53 Aligned_cols=27 Identities=4% Similarity=-0.065 Sum_probs=22.3
Q ss_pred hHHHHHHHHHHhCCCCCCCCCCCCcccccccCCc
Q psy12666 55 FVNKLIVKCQIVNPYLDSSKAFDKPCHMHELWPG 88 (347)
Q Consensus 55 SYa~LI~~AI~ssP~~~~~~~~~k~LTL~EIY~~ 88 (347)
+|..||.+||...-+ .+..++..|..|
T Consensus 6 ~y~~MI~eAI~~l~e-------r~GsS~~aI~ky 32 (88)
T cd00073 6 PYSEMVTEAIKALKE-------RKGSSLQAIKKY 32 (88)
T ss_pred CHHHHHHHHHHHcCC-------CCCcCHHHHHHH
Confidence 689999999987665 467889999984
No 17
>PF05265 DUF723: Protein of unknown function (DUF723); InterPro: IPR007929 This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA binding.
Probab=20.83 E-value=35 Score=26.74 Aligned_cols=13 Identities=31% Similarity=0.728 Sum_probs=11.3
Q ss_pred CCCccccCCcccc
Q psy12666 275 PCPHHLVNSCNCH 287 (347)
Q Consensus 275 ~c~~h~~~~c~c~ 287 (347)
+||+|+.+.|+=.
T Consensus 34 ~CP~HG~~~~s~~ 46 (60)
T PF05265_consen 34 RCPKHGNFTCSTF 46 (60)
T ss_pred ECCCCCcEEeccH
Confidence 8999999998754
Done!