Query psy13845
Match_columns 430
No_of_seqs 249 out of 435
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 21:53:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13845.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13845hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3701|consensus 100.0 1.3E-69 2.9E-74 549.7 20.8 325 59-421 1-334 (411)
2 cd00049 MH1 MH1 is a small DNA 100.0 7.6E-47 1.6E-51 328.8 9.7 119 68-190 1-121 (121)
3 smart00523 DWA Domain A in dwa 100.0 2E-44 4.4E-49 308.4 9.3 108 81-192 1-109 (109)
4 PF03165 MH1: MH1 domain; Int 100.0 4E-42 8.6E-47 292.4 2.4 101 86-189 1-103 (103)
5 KOG3701|consensus 100.0 1.7E-33 3.6E-38 286.5 13.0 203 214-428 68-297 (411)
6 cd00050 MH2 MH2 domain; C term 99.9 4.2E-25 9.1E-30 204.1 4.3 91 310-401 1-96 (176)
7 smart00524 DWB Domain B in dwa 99.9 4.2E-23 9.2E-28 190.0 4.0 86 315-401 1-91 (171)
8 PF03166 MH2: MH2 domain; Int 99.8 1.2E-20 2.5E-25 176.0 2.7 91 311-401 1-96 (181)
9 cd00050 MH2 MH2 domain; C term 99.8 1.5E-19 3.3E-24 167.2 5.0 75 350-428 4-78 (176)
10 smart00524 DWB Domain B in dwa 99.7 7.3E-19 1.6E-23 162.0 4.4 72 353-428 2-73 (171)
11 smart00523 DWA Domain A in dwa 99.6 1.8E-16 3.9E-21 136.2 2.2 62 215-277 44-105 (109)
12 PF03165 MH1: MH1 domain; Int 99.5 2.9E-16 6.2E-21 134.0 -2.3 62 214-276 40-101 (103)
13 cd00049 MH1 MH1 is a small DNA 99.5 1.7E-15 3.6E-20 132.5 2.2 58 218-276 61-118 (121)
14 PF03166 MH2: MH2 domain; Int 99.5 4.6E-15 1E-19 138.4 3.8 74 351-428 4-78 (181)
15 KOG3663|consensus 79.7 1.9 4E-05 45.3 3.6 82 91-186 73-169 (518)
16 PF07624 PSD2: Protein of unkn 56.5 18 0.0004 29.0 4.1 48 65-112 23-71 (76)
17 PF00498 FHA: FHA domain; Int 50.5 33 0.00071 26.0 4.5 23 2-24 24-48 (68)
18 KOG2884|consensus 39.2 63 0.0014 31.8 5.4 56 68-123 92-174 (259)
19 PHA00008 J DNA packaging prote 38.8 21 0.00044 23.1 1.4 13 417-429 13-25 (26)
20 PF10401 IRF-3: Interferon-reg 33.1 86 0.0019 29.0 5.2 45 1-50 76-120 (180)
21 PF04726 Microvir_J: Microviru 30.3 19 0.0004 22.8 0.2 12 417-428 12-23 (24)
22 PF10709 DUF2511: Protein of u 26.4 69 0.0015 26.9 2.9 27 5-31 13-39 (87)
23 smart00240 FHA Forkhead associ 24.3 88 0.0019 22.0 2.9 23 2-24 25-49 (52)
No 1
>KOG3701|consensus
Probab=100.00 E-value=1.3e-69 Score=549.71 Aligned_cols=325 Identities=43% Similarity=0.705 Sum_probs=239.3
Q ss_pred ccccCCCChHHHHHHhhccc-CCCCcchhHHHHHHHHHHhhcc-CCHHHHHHHHhcCC-CCccceEecCCCCCCCCcccC
Q psy13845 59 MTSLFPFTPPIVKKLLGWKK-GDGEDKYSEKAVKSLVKKLKKS-NGLDELEKAITTQD-PNTKCVTIPSARTDKGSTDLS 135 (430)
Q Consensus 59 ~~~~~~~~~~~v~~ll~~~~-g~~~~~~~~ka~~~l~Kklk~~-~~le~L~~Av~~~~-~~t~Cv~i~~~r~~dgrl~~~ 135 (430)
++++++|+.|+|++||+||| |+++|+|++||+++|||||||+ ++||+|++||++++ .+++||||| |++|||||++
T Consensus 1 ~~~~~~~~~p~v~~~~~~r~~~~~~e~~~~ka~~slvkklk~~~~~le~l~~av~s~g~~~~~Cvtip--rslD~Rlq~~ 78 (411)
T KOG3701|consen 1 TSSLLPFTGPAVKDLLGPRQLGGEDEKFAEKAVESLVKKLKDKKGELENLIKAVESPGTKPTGCVTIP--RSLDGRLQVA 78 (411)
T ss_pred CCcccCCCCcchhhccCccccCchhHHHHHHHHHHHHHHhhcccchHHHHHHHhcCCCCCCCceEECC--CCCCcccccc
Confidence 35789999999999999999 9999999999999999999997 67999999999995 569999999 9999999999
Q ss_pred CCCCCCCceEeeeeecCCCCCCCcccccccccccccCCCCCeeecCccchhceeec-Ccccccccccccccccccccccc
Q psy13845 136 NRSKGLPHVIYCRLWRWPSLQSHNELRSIDLCAFGFSLKRDQVCVNPYHYQRIHTQ-GICTCNVEREELGKMVENLTKNA 214 (430)
Q Consensus 136 ~~~k~~Phv~~crl~RwpdL~~~~eLk~l~~C~~~~~~~~~~vC~NPyHy~rv~~p-~~pp~~v~~~~l~e~~~~~~~~~ 214 (430)
+| |++|||||||||||||||+++|||++++|+++|+++.++||||||||+||+.| ..+|.++.+.. +.......
T Consensus 79 ~r-kg~Phviy~rlwRwpdl~~~~elk~l~~C~~a~~~~~~~vC~NPyHy~rv~~~~~~~~~~~~~~~--~~~~~~~~-- 153 (411)
T KOG3701|consen 79 HR-KGFPHVIYCRLWRWPDLQKNHELKRLECCEHAFESKSDNVCINPYHYSRVESPPILPPPLSPNSP--PNDALKTL-- 153 (411)
T ss_pred CC-CCCCceEEEEeecccccccchhheecccCCccccCCCCCeeeCCcccceeecCCCCCcccCCCCC--ccccccch--
Confidence 99 99999999999999999999999999999999999999999999999999999 56666666532 11111100
Q ss_pred cCCCCCCccCCCCCCCCcccccccccCCCccCCCccccccccccCccCCCCccccCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy13845 215 RTDKGSTDLSNRSKGLPHVIYCRLWRWPSLQSHNELRSIDLCAFGFSLKRDQVCVNPYHYQRIHGGYMSEDGDATDALSL 294 (430)
Q Consensus 215 rs~dg~~~l~~~~k~lPhvi~cRLwRWPDLqs~~eLk~l~~C~~~~~~~~~~vc~NPyhyesppP~y~s~~~~~~~~~~~ 294 (430)
.+++...+ . ...+|++... +++... .+ ..+|-....+.| ....++..+...+
T Consensus 154 -~~~~~~~~-~-~~~~P~n~~~-----~~~~~~-----------~~-------~~tp~~~~~~~P--~~~~~p~s~~~~~ 205 (411)
T KOG3701|consen 154 -LDDGGVDI-V-NRSMPQNNHS-----SDLIGP-----------HA-------PHTPDSSQIPAP--LGDGGPSSDSSAL 205 (411)
T ss_pred -hhcccccc-c-ccCCCccccc-----cccccc-----------CC-------CCCCCcccCCCC--CCCCCCCCccccc
Confidence 11111111 1 1234444332 111000 00 000000011111 0000111110000
Q ss_pred CCCCCCCCCCCCCccccCCCccccccccccccccccccccCCCccccCCccCCCCCcccccccccCcccchhHhhhhccc
Q psy13845 295 SPSPAIPAGDTQPVMYCEPVFWCSISYYELNTRVGETFHASQPSISVDGFTDPSNSERFCLGLLSNVNRNHVVEQIRRHI 374 (430)
Q Consensus 295 ~p~~~~~~~~~~pv~y~eP~~WCSIaY~El~~rVGe~F~vs~psV~VDGftDPS~~~rfCLg~lsnvnR~~~vE~tR~~I 374 (430)
.+. +....+..|+.|+++++||+|+|||+++||||+|++..++++||||+|||+++|||||+++|+||++++|++|+||
T Consensus 206 ~~~-P~~~P~~~~~~~~~~~~WcsIaYyEl~~rVGE~f~v~~~~~~vDG~~dps~~~rfcLgqlsn~~Rn~~~e~~R~~I 284 (411)
T KOG3701|consen 206 PGL-PTDSPDVGPVHYEEPKSWCSIAYYELNTRVGETFHVPGPSITVDGFTDPSNGSRFCLGQLSNVNRNEKVEKTRAHI 284 (411)
T ss_pred CCC-CCCCCccCcccccCCcceeEEEEeeccccccceEEecCCceEEeeeecCCCCCceeeccccCCCccchhHHHHhhc
Confidence 000 1001144557899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCceeeeecccCC-----CCCCceEeecccCCCCchhHHHhhhccCCceEE
Q psy13845 375 GKGPSISVDGFTDP-----SNSERFCLGLLSNVNRNHVVEQIRRHIGKGVRS 421 (430)
Q Consensus 375 GkGvsL~vdGftDp-----~~~~~fcLg~l~n~~r~~~v~~tR~~iG~Gv~L 421 (430)
|+||+|++.+ +|+ ++...|..+--.|-.-..+- .|+++|=.|=.|
T Consensus 285 G~GV~L~~~~-gdVw~~n~sd~pIFVqS~~ln~~~g~~~-~~v~ki~Pg~~i 334 (411)
T KOG3701|consen 285 GKGVQLSYEN-GDVWLYNLSDYPIFVQSPNLNYPNGRTL-DTVHKVPPGYSI 334 (411)
T ss_pred cCceeeeEec-CcEEEEecCCCceeeeCCCCcCCCCCcc-cceEeeCCCcee
Confidence 9999999999 776 45556877765554433444 666666555433
No 2
>cd00049 MH1 MH1 is a small DNA binding domain, binding in an unusal way involving a beta hairpin structure binding to the major groove. MH1 is present in Smad proteins, an important family of proteins involved in TGF-beta signalling and frequent targets of tumorigenic mutations. Also known as Domain A in dwarfin family proteins.
Probab=100.00 E-value=7.6e-47 Score=328.83 Aligned_cols=119 Identities=54% Similarity=1.045 Sum_probs=113.2
Q ss_pred HHHHHHhhccc-CCCCcchhHHHHHHHHHHhhccCCHHHHHHHHhcC-CCCccceEecCCCCCCCCcccCCCCCCCCceE
Q psy13845 68 PIVKKLLGWKK-GDGEDKYSEKAVKSLVKKLKKSNGLDELEKAITTQ-DPNTKCVTIPSARTDKGSTDLSNRSKGLPHVI 145 (430)
Q Consensus 68 ~~v~~ll~~~~-g~~~~~~~~ka~~~l~Kklk~~~~le~L~~Av~~~-~~~t~Cv~i~~~r~~dgrl~~~~~~k~~Phv~ 145 (430)
++|++||+|++ |+++|+|++||+++|||||||+.+||+|++||+++ +.+|+||+|| |+ |||||+++| +++|||+
T Consensus 1 ~~~~~ll~~~~~~~~~e~~~~k~~~sLlKkLKk~~~le~L~~AV~s~g~~~t~CV~i~--r~-D~rl~~~~r-~~~phv~ 76 (121)
T cd00049 1 ALVKRLLGEKKIGGEEEKWKKKAAESLLKKLKKKIQLEELEDAVESRGGPPTRCVLIP--RS-DGRLQVSHR-KGLPHVI 76 (121)
T ss_pred ChhHHhhcccccCcchHHHHHHHHHHHHHHHhcccCHHHHHHHHHcCCCCCCCeEEec--cc-ccccccccc-CCCcceE
Confidence 37999999999 89999999999999999999856999999999999 5669999999 87 999999999 9999999
Q ss_pred eeeeecCCCCCCCcccccccccccccCCCCCeeecCccchhceee
Q psy13845 146 YCRLWRWPSLQSHNELRSIDLCAFGFSLKRDQVCVNPYHYQRIHT 190 (430)
Q Consensus 146 ~crl~RwpdL~~~~eLk~l~~C~~~~~~~~~~vC~NPyHy~rv~~ 190 (430)
||||||||||++++|||++++|+++|+++.++||||||||+||+.
T Consensus 77 ~crlwRWpDL~~~~eLk~l~~C~~~~~~~~~~vC~NPyHy~rv~~ 121 (121)
T cd00049 77 YCRVWRWPDLRSNHELKRLETCEHAFDSKPDEVCINPYHYSRVVR 121 (121)
T ss_pred EEeeeeccccCchHhheeCccCCCccccCCCeEEeCCceeeeecC
Confidence 999999999999999999999999999999999999999999974
No 3
>smart00523 DWA Domain A in dwarfin family proteins.
Probab=100.00 E-value=2e-44 Score=308.43 Aligned_cols=108 Identities=50% Similarity=0.971 Sum_probs=103.5
Q ss_pred CCcchhHHHHHHHHHHhhccCCHHHHHHHHhcCC-CCccceEecCCCCCCCCcccCCCCCCCCceEeeeeecCCCCCCCc
Q psy13845 81 GEDKYSEKAVKSLVKKLKKSNGLDELEKAITTQD-PNTKCVTIPSARTDKGSTDLSNRSKGLPHVIYCRLWRWPSLQSHN 159 (430)
Q Consensus 81 ~~~~~~~ka~~~l~Kklk~~~~le~L~~Av~~~~-~~t~Cv~i~~~r~~dgrl~~~~~~k~~Phv~~crl~RwpdL~~~~ 159 (430)
.+|+|++||+++|+||||+ ++||+|++||++++ .+|+||+|| |++|||||++++ +++|||+||||||||||+|++
T Consensus 1 ~~ek~~~k~~~sL~KklK~-k~le~L~~AV~s~g~~~t~CV~i~--~~~dgrl~~~~~-~~~phvi~crLfRWpdL~s~~ 76 (109)
T smart00523 1 VEEKWAKKATESLLKKLKK-KQLEELLQAVESKGGPPTRCVLIP--RSLDGRLQVAHR-KGLPHVLYCRLFRWPDLQSPH 76 (109)
T ss_pred CcHHHHHHHHHHHHHHHHH-HHHHHHHHHHHcCCCCCCCeEEeC--cccCcccccccC-CCCCcEEEEEEeeCCCCCCHH
Confidence 3789999999999999998 69999999999995 789999999 999999999999 999999999999999999999
Q ss_pred ccccccccccccCCCCCeeecCccchhceeecC
Q psy13845 160 ELRSIDLCAFGFSLKRDQVCVNPYHYQRIHTQG 192 (430)
Q Consensus 160 eLk~l~~C~~~~~~~~~~vC~NPyHy~rv~~p~ 192 (430)
|||+++.|+++|++++++||||||||+||+.|+
T Consensus 77 eLk~l~~C~~~~~~~~~~vC~NPyHy~rv~~p~ 109 (109)
T smart00523 77 ELKALPTCEHAFESKSDEVCCNPYHYSRVERPE 109 (109)
T ss_pred HceecccCCCcccCCCCeEEeCCceEEEeecCC
Confidence 999999999999999999999999999999874
No 4
>PF03165 MH1: MH1 domain; InterPro: IPR003619 Mammalian dwarfins are phosphorylated in response to transforming growth factor beta and are implicated in control of cell growth []. The dwarfin family also includes the Drosophila protein MAD that is required for the function of decapentaplegic (DPP) and may play a role in DPP signalling. Drosophila Mad binds to DNA and directly mediates activation of vestigial by Dpp []. This domain is also found in nuclear factor I (NF-I) or CCAAT box-binding transcription factor (CTF). This entry represents the MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved 11 residue beta hairpin is used to bind the DNA consensus sequence GNCN in the major groove, shown to be vital for the transcriptional activation of target genes. Not all examples of MH1 can bind to DNA however. Smad2 cannot bind DNA and has a large insertion within the hairpin that presumably abolishes DNA binding. A basic helix (H2) in MH1 with the nuclear localisation signal KKLKK has been shown to be essential for Smad3 nuclear import. Smads also use the MH1 domain to interact with transcription factors such as Jun, TFE3, Sp1, and Runx [, , ].; GO: 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3QSV_A 1MHD_A 1OZJ_A 3KMP_B.
Probab=100.00 E-value=4e-42 Score=292.37 Aligned_cols=101 Identities=58% Similarity=1.103 Sum_probs=79.1
Q ss_pred hHHHHHHHHHHhhcc-CCHHHHHHHHhcC-CCCccceEecCCCCCCCCcccCCCCCCCCceEeeeeecCCCCCCCccccc
Q psy13845 86 SEKAVKSLVKKLKKS-NGLDELEKAITTQ-DPNTKCVTIPSARTDKGSTDLSNRSKGLPHVIYCRLWRWPSLQSHNELRS 163 (430)
Q Consensus 86 ~~ka~~~l~Kklk~~-~~le~L~~Av~~~-~~~t~Cv~i~~~r~~dgrl~~~~~~k~~Phv~~crl~RwpdL~~~~eLk~ 163 (430)
++||+++|||||||+ ++||+|++||+|+ +.+|+||+|| |++|||||++++ |++||||||||||||||++++|||+
T Consensus 1 ~~k~~~sLlkkLK~~~~~le~L~~Av~s~g~~~t~CV~i~--r~~dgrl~v~~~-k~~phvl~crlwRwpdL~~~~eLk~ 77 (103)
T PF03165_consen 1 CEKAIKSLLKKLKKKIGQLEELLKAVESRGDPPTKCVTIP--RSLDGRLQVSGR-KGLPHVLYCRLWRWPDLRHSHELKR 77 (103)
T ss_dssp HHHHHHHHHHHHTTTCTHHHHHHHHHHCTTTSTS---EEE----TTS-EEETTE-EE-HHHHHHHHHT-TT--SCCCEEE
T ss_pred ChHHHHHHHHHHccccchHHHHHHHHhcCCCCCCCcEEec--CccCcccccccc-ccCceEEEEEEechhhcCCHHhccc
Confidence 489999999999996 6999999999988 7899999999 999999999999 9999999999999999999999999
Q ss_pred ccccccccCCCCCeeecCccchhcee
Q psy13845 164 IDLCAFGFSLKRDQVCVNPYHYQRIH 189 (430)
Q Consensus 164 l~~C~~~~~~~~~~vC~NPyHy~rv~ 189 (430)
++.|+++|+.++++||||||||+|||
T Consensus 78 l~~C~~~~~~~~~~vC~NPyHy~rv~ 103 (103)
T PF03165_consen 78 LPHCRFAFDSKNDEVCCNPYHYSRVC 103 (103)
T ss_dssp -TT-TT-GGG--SEEE--GGGEEE--
T ss_pred CCCCCChhhcCCCCEEeCCcEeeecC
Confidence 99999999999999999999999986
No 5
>KOG3701|consensus
Probab=100.00 E-value=1.7e-33 Score=286.48 Aligned_cols=203 Identities=36% Similarity=0.582 Sum_probs=132.2
Q ss_pred ccCCCCCCccCCCCCCCCcccccccccCCCccCCCccccccccccCccCCCCccccCCCCCCC---C---CCCCCCCCCC
Q psy13845 214 ARTDKGSTDLSNRSKGLPHVIYCRLWRWPSLQSHNELRSIDLCAFGFSLKRDQVCVNPYHYQR---I---HGGYMSEDGD 287 (430)
Q Consensus 214 ~rs~dg~~~l~~~~k~lPhvi~cRLwRWPDLqs~~eLk~l~~C~~~~~~~~~~vc~NPyhyes---p---pP~y~s~~~~ 287 (430)
+|++|||.+.++ +|++||++||||||||||+.++|||+++.|++++.++++.||+|||||++ + +|++.+...+
T Consensus 68 prslD~Rlq~~~-rkg~Phviy~rlwRwpdl~~~~elk~l~~C~~a~~~~~~~vC~NPyHy~rv~~~~~~~~~~~~~~~~ 146 (411)
T KOG3701|consen 68 PRSLDGRLQVAH-RKGFPHVIYCRLWRWPDLQKNHELKRLECCEHAFESKSDNVCINPYHYSRVESPPILPPPLSPNSPP 146 (411)
T ss_pred CCCCCccccccC-CCCCCceEEEEeecccccccchhheecccCCccccCCCCCeeeCCcccceeecCCCCCcccCCCCCc
Confidence 478899988765 79999999999999999999999999999999999888899999999942 2 2222221100
Q ss_pred CC--CC-----CCC--CCCCCCC--CC-------CCCCc-c-ccCCCcccccccccccc-ccccccccCCCccccCCccC
Q psy13845 288 AT--DA-----LSL--SPSPAIP--AG-------DTQPV-M-YCEPVFWCSISYYELNT-RVGETFHASQPSISVDGFTD 346 (430)
Q Consensus 288 ~~--~~-----~~~--~p~~~~~--~~-------~~~pv-~-y~eP~~WCSIaY~El~~-rVGe~F~vs~psV~VDGftD 346 (430)
.. .. ... .++++.. .. +..|- . ...| ...-.+... ..-..+...+|.+. -..
T Consensus 147 ~~~~~~~~~~~~~~~~~~~~P~n~~~~~~~~~~~~~tp~~~~~~~P----~~~~~p~s~~~~~~~~P~~~P~~~---~~~ 219 (411)
T KOG3701|consen 147 NDALKTLLDDGGVDIVNRSMPQNNHSSDLIGPHAPHTPDSSQIPAP----LGDGGPSSDSSALPGLPTDSPDVG---PVH 219 (411)
T ss_pred cccccchhhcccccccccCCCcccccccccccCCCCCCCcccCCCC----CCCCCCCCcccccCCCCCCCCccC---ccc
Confidence 00 00 000 0100000 00 00000 0 0111 000000000 00000010111111 112
Q ss_pred CCCCcccccccccCcccchhHhhhhccccCCceeeeecccCCCCCCceEeecccCCCCchhHHHhhhccCCceEEEeecc
Q psy13845 347 PSNSERFCLGLLSNVNRNHVVEQIRRHIGKGPSISVDGFTDPSNSERFCLGLLSNVNRNHVVEQIRRHIGKGVRSLSVAK 426 (430)
Q Consensus 347 PS~~~rfCLg~lsnvnR~~~vE~tR~~IGkGvsL~vdGftDp~~~~~fcLg~l~n~~r~~~v~~tR~~iG~Gv~L~y~~g 426 (430)
......||.++ |++.+++++|.|.++ +.++++|||+||++++|||||+|+|+||+.++|+||+|||+||+|||++|
T Consensus 220 ~~~~~~WcsIa-YyEl~~rVGE~f~v~---~~~~~vDG~~dps~~~rfcLgqlsn~~Rn~~~e~~R~~IG~GV~L~~~~g 295 (411)
T KOG3701|consen 220 YEEPKSWCSIA-YYELNTRVGETFHVP---GPSITVDGFTDPSNGSRFCLGQLSNVNRNEKVEKTRAHIGKGVQLSYENG 295 (411)
T ss_pred ccCCcceeEEE-EeeccccccceEEec---CCceEEeeeecCCCCCceeeccccCCCccchhHHHHhhccCceeeeEecC
Confidence 22445677765 666679999999985 66999999999999999999999999999999999999999999999999
Q ss_pred cc
Q psy13845 427 EK 428 (430)
Q Consensus 427 ~~ 428 (430)
|-
T Consensus 296 dV 297 (411)
T KOG3701|consen 296 DV 297 (411)
T ss_pred cE
Confidence 84
No 6
>cd00050 MH2 MH2 domain; C terminal domain of SMAD family proteins, responsible for receptor interaction, transactivation, and homo- and heterooligomerisation; also known as Domain B in dwarfin family proteins
Probab=99.91 E-value=4.2e-25 Score=204.06 Aligned_cols=91 Identities=59% Similarity=0.975 Sum_probs=84.5
Q ss_pred ccCCCccccccccccccccccccccCCCccccCCccCCCCCcccccccccCcccchhHhhhhccccCCceeeeecccCC-
Q psy13845 310 YCEPVFWCSISYYELNTRVGETFHASQPSISVDGFTDPSNSERFCLGLLSNVNRNHVVEQIRRHIGKGPSISVDGFTDP- 388 (430)
Q Consensus 310 y~eP~~WCSIaY~El~~rVGe~F~vs~psV~VDGftDPS~~~rfCLg~lsnvnR~~~vE~tR~~IGkGvsL~vdGftDp- 388 (430)
+++|++||+|||||+++||||+|+++.++++||||+||++++|||||+++|++|++.+|++|+|||+||+|++++ +|+
T Consensus 1 ~~~~~~WCsIaY~El~~RVGe~f~~~~~~~~VDGf~d~~~~~rfcLg~lsn~~R~~~ve~~R~~IG~Gv~L~~~~-g~Vw 79 (176)
T cd00050 1 PSEPEHWCSIAYYELNTRVGETFKVSGPNITVDGFTDPSNGSRFCLGQLSNVNRNETVEKTRRHIGKGVQLSYEN-GEVW 79 (176)
T ss_pred CCCCCceEEEEEEEccceecccEeccCCcEEEEecccCCCCCEEEecccCCCCCcHHHHHHHHhccCCEEEEEeC-CeEE
Confidence 358999999999999999999999999999999999999999999999999999999999999999999999998 676
Q ss_pred ----CCCCceEeecccC
Q psy13845 389 ----SNSERFCLGLLSN 401 (430)
Q Consensus 389 ----~~~~~fcLg~l~n 401 (430)
|+...|+.+--.|
T Consensus 80 ~~~~S~~~VFVqS~~l~ 96 (176)
T cd00050 80 AYNLSDHPIFVQSPTLD 96 (176)
T ss_pred EEEcCCCCEEEcCCCCC
Confidence 7788888876544
No 7
>smart00524 DWB Domain B in dwarfin family proteins.
Probab=99.87 E-value=4.2e-23 Score=189.96 Aligned_cols=86 Identities=60% Similarity=1.006 Sum_probs=78.8
Q ss_pred ccccccccccccccccccccCCCccccCCccCCCCCcccccccccCcccchhHhhhhccccCCceeeeecccCC-----C
Q psy13845 315 FWCSISYYELNTRVGETFHASQPSISVDGFTDPSNSERFCLGLLSNVNRNHVVEQIRRHIGKGPSISVDGFTDP-----S 389 (430)
Q Consensus 315 ~WCSIaY~El~~rVGe~F~vs~psV~VDGftDPS~~~rfCLg~lsnvnR~~~vE~tR~~IGkGvsL~vdGftDp-----~ 389 (430)
+||+|+|||+++||||+|+++.++|+||||+||++++|||||+++|+||+..+|++|+|||+||+|++++ +|+ |
T Consensus 1 ~WcsIaYyEl~~rVGe~f~~~~p~v~Vdgf~d~~~~~rfcLg~lsn~nR~~~~~~~R~~IG~Gv~L~~~~-g~Vw~~~~s 79 (171)
T smart00524 1 SWCSIAYYELNTRVGETFKVSSPSVTVDGFTDPSDGNRFCLGQLSNVNRNEATELIRKHIGKGVQLSYEN-GDVWLYNRS 79 (171)
T ss_pred CCcEEEEEEecccccceEEccCCeEEEEecccCCCCCeeEeccCCCCCccHHHHHHHHhccCceEEEEeC-CeEEEEEcC
Confidence 6999999999999999999999999999999999999999999999999999999999999999999998 665 6
Q ss_pred CCCceEeecccC
Q psy13845 390 NSERFCLGLLSN 401 (430)
Q Consensus 390 ~~~~fcLg~l~n 401 (430)
+...|..+--.|
T Consensus 80 ~~~VFVqS~~~~ 91 (171)
T smart00524 80 DSPIFVQSPYLD 91 (171)
T ss_pred CCCeEEcCCCcc
Confidence 666777665544
No 8
>PF03166 MH2: MH2 domain; InterPro: IPR001132 Mammalian dwarfins are phosphorylated in response to transforming growth factor beta and are implicated in control of cell growth []. The dwarfin family also includes the Drosophila protein MAD that is required for the function of decapentaplegic (DPP) and may play a role in DPP signalling. Drosophila Mad binds to DNA and directly mediates activation of vestigial by Dpp []. This domain is also found in nuclear factor I (NF-I) or CCAAT box-binding transcription factor (CTF). This entry represents the SMAD (Mothers against decapentaplegic (MAD) homologue) (also called MH2 for MAD homology 2) domain found at the carboxy terminus of MAD related proteins such as Smads. This domain is separated from the MH1 domain by a non-conserved linker region. The MH2 domain mediates interaction with a wide variety of proteins and provides specificity and selectivity to Smad function and also is critical for mediating interactions in Smad oligomers. Unlike MH1, MH2 does not bind DNA. The well-studied MH2 domain of Smad4 is composed of five alpha helices and three loops enclosing a beta sandwich. Smads are involved in the propagation of TGF-beta signals by direct association with the TGF-beta receptor kinase which phosphorylates the last two Ser of a conserved 'SSXS' motif located at the C terminus of MH2 [, , ].; GO: 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1MK2_A 1U7F_A 1MJS_A 1KHU_A 1DD1_C 1G88_A 1U7V_B 1MR1_B 1YGS_A 3DIT_B ....
Probab=99.80 E-value=1.2e-20 Score=176.01 Aligned_cols=91 Identities=57% Similarity=0.948 Sum_probs=75.2
Q ss_pred cCCCccccccccccccccccccccCCCccccCCccCCCCCcccccccccCcccchhHhhhhccccCCceeeeecccCC--
Q psy13845 311 CEPVFWCSISYYELNTRVGETFHASQPSISVDGFTDPSNSERFCLGLLSNVNRNHVVEQIRRHIGKGPSISVDGFTDP-- 388 (430)
Q Consensus 311 ~eP~~WCSIaY~El~~rVGe~F~vs~psV~VDGftDPS~~~rfCLg~lsnvnR~~~vE~tR~~IGkGvsL~vdGftDp-- 388 (430)
+++++||+|+|||+++|||++|++..++|+||||+||+.++|||||.++|++|+..++++|+|||+||.|++++.+++
T Consensus 1 ~~~~~Wc~I~Y~E~~~rVG~~f~~~~~~v~idG~~d~~~~~r~~Lg~~~n~~R~~~~~~~R~~IG~Gi~l~~~~~G~V~l 80 (181)
T PF03166_consen 1 EEPEIWCSIAYYELNTRVGEAFKARSPSVIIDGFTDPSDGDRFCLGQLSNVNRDSKTEKIRRHIGKGIKLSYEEDGNVWL 80 (181)
T ss_dssp -S-SSSEEEEEEETTEEESEEEEEESSEEEEESSSSSSSSSEEECTT---TT--HHHHHHHTTCTT-EEEEEETTTEEEE
T ss_pred CCCCeeEEEEEEecCCeEcceeEccCCeEEEeeccCCCCCCcEecCccCCCCCChHHhhHHheecCcEEEEEecCCeEEE
Confidence 368899999999999999999999999999999999999999999999999999999999999999999999966554
Q ss_pred ---CCCCceEeecccC
Q psy13845 389 ---SNSERFCLGLLSN 401 (430)
Q Consensus 389 ---~~~~~fcLg~l~n 401 (430)
++...|+++...|
T Consensus 81 ~n~s~~pVFVqS~~~n 96 (181)
T PF03166_consen 81 YNRSDSPVFVQSPTLN 96 (181)
T ss_dssp EE-SSS-EEEE-HHHH
T ss_pred EECCCCCEEEccCCCC
Confidence 7788999887665
No 9
>cd00050 MH2 MH2 domain; C terminal domain of SMAD family proteins, responsible for receptor interaction, transactivation, and homo- and heterooligomerisation; also known as Domain B in dwarfin family proteins
Probab=99.77 E-value=1.5e-19 Score=167.23 Aligned_cols=75 Identities=52% Similarity=0.771 Sum_probs=67.2
Q ss_pred CcccccccccCcccchhHhhhhccccCCceeeeecccCCCCCCceEeecccCCCCchhHHHhhhccCCceEEEeecccc
Q psy13845 350 SERFCLGLLSNVNRNHVVEQIRRHIGKGPSISVDGFTDPSNSERFCLGLLSNVNRNHVVEQIRRHIGKGVRSLSVAKEK 428 (430)
Q Consensus 350 ~~rfCLg~lsnvnR~~~vE~tR~~IGkGvsL~vdGftDp~~~~~fcLg~l~n~~r~~~v~~tR~~iG~Gv~L~y~~g~~ 428 (430)
.+.||..+ |++.+++++|.++++ +.++++|||+||++++|||||+|+|++|+++||+||+|||+||+|+|++||.
T Consensus 4 ~~~WCsIa-Y~El~~RVGe~f~~~---~~~~~VDGf~d~~~~~rfcLg~lsn~~R~~~ve~~R~~IG~Gv~L~~~~g~V 78 (176)
T cd00050 4 PEHWCSIA-YYELNTRVGETFKVS---GPNITVDGFTDPSNGSRFCLGQLSNVNRNETVEKTRRHIGKGVQLSYENGEV 78 (176)
T ss_pred CCceEEEE-EEEccceecccEecc---CCcEEEEecccCCCCCEEEecccCCCCCcHHHHHHHHhccCCEEEEEeCCeE
Confidence 35688866 556678999999764 6789999999999999999999999999999999999999999999999985
No 10
>smart00524 DWB Domain B in dwarfin family proteins.
Probab=99.74 E-value=7.3e-19 Score=162.01 Aligned_cols=72 Identities=47% Similarity=0.729 Sum_probs=65.6
Q ss_pred cccccccCcccchhHhhhhccccCCceeeeecccCCCCCCceEeecccCCCCchhHHHhhhccCCceEEEeecccc
Q psy13845 353 FCLGLLSNVNRNHVVEQIRRHIGKGPSISVDGFTDPSNSERFCLGLLSNVNRNHVVEQIRRHIGKGVRSLSVAKEK 428 (430)
Q Consensus 353 fCLg~lsnvnR~~~vE~tR~~IGkGvsL~vdGftDp~~~~~fcLg~l~n~~r~~~v~~tR~~iG~Gv~L~y~~g~~ 428 (430)
||..+ |++.+++++|.+.++ +.+++||||+||++++|||||+|+|+||++++|+||+|||+||+|+|++||.
T Consensus 2 WcsIa-YyEl~~rVGe~f~~~---~p~v~Vdgf~d~~~~~rfcLg~lsn~nR~~~~~~~R~~IG~Gv~L~~~~g~V 73 (171)
T smart00524 2 WCSIA-YYELNTRVGETFKVS---SPSVTVDGFTDPSDGNRFCLGQLSNVNRNEATELIRKHIGKGVQLSYENGDV 73 (171)
T ss_pred CcEEE-EEEecccccceEEcc---CCeEEEEecccCCCCCeeEeccCCCCCccHHHHHHHHhccCceEEEEeCCeE
Confidence 78765 556679999988764 6899999999999999999999999999999999999999999999999984
No 11
>smart00523 DWA Domain A in dwarfin family proteins.
Probab=99.61 E-value=1.8e-16 Score=136.24 Aligned_cols=62 Identities=52% Similarity=1.115 Sum_probs=54.0
Q ss_pred cCCCCCCccCCCCCCCCcccccccccCCCccCCCccccccccccCccCCCCccccCCCCCCCC
Q psy13845 215 RTDKGSTDLSNRSKGLPHVIYCRLWRWPSLQSHNELRSIDLCAFGFSLKRDQVCVNPYHYQRI 277 (430)
Q Consensus 215 rs~dg~~~l~~~~k~lPhvi~cRLwRWPDLqs~~eLk~l~~C~~~~~~~~~~vc~NPyhyesp 277 (430)
++.||+.+++ .+++.||++||||||||||++++||++++.|++++++++++||+|||||+..
T Consensus 44 ~~~dgrl~~~-~~~~~phvi~crLfRWpdL~s~~eLk~l~~C~~~~~~~~~~vC~NPyHy~rv 105 (109)
T smart00523 44 RSLDGRLQVA-HRKGLPHVLYCRLFRWPDLQSPHELKALPTCEHAFESKSDEVCCNPYHYSRV 105 (109)
T ss_pred cccCcccccc-cCCCCCcEEEEEEeeCCCCCCHHHceecccCCCcccCCCCeEEeCCceEEEe
Confidence 4567776553 3478999999999999999999999999999999988999999999999643
No 12
>PF03165 MH1: MH1 domain; InterPro: IPR003619 Mammalian dwarfins are phosphorylated in response to transforming growth factor beta and are implicated in control of cell growth []. The dwarfin family also includes the Drosophila protein MAD that is required for the function of decapentaplegic (DPP) and may play a role in DPP signalling. Drosophila Mad binds to DNA and directly mediates activation of vestigial by Dpp []. This domain is also found in nuclear factor I (NF-I) or CCAAT box-binding transcription factor (CTF). This entry represents the MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved 11 residue beta hairpin is used to bind the DNA consensus sequence GNCN in the major groove, shown to be vital for the transcriptional activation of target genes. Not all examples of MH1 can bind to DNA however. Smad2 cannot bind DNA and has a large insertion within the hairpin that presumably abolishes DNA binding. A basic helix (H2) in MH1 with the nuclear localisation signal KKLKK has been shown to be essential for Smad3 nuclear import. Smads also use the MH1 domain to interact with transcription factors such as Jun, TFE3, Sp1, and Runx [, , ].; GO: 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3QSV_A 1MHD_A 1OZJ_A 3KMP_B.
Probab=99.54 E-value=2.9e-16 Score=134.02 Aligned_cols=62 Identities=53% Similarity=1.176 Sum_probs=41.6
Q ss_pred ccCCCCCCccCCCCCCCCcccccccccCCCccCCCccccccccccCccCCCCccccCCCCCCC
Q psy13845 214 ARTDKGSTDLSNRSKGLPHVIYCRLWRWPSLQSHNELRSIDLCAFGFSLKRDQVCVNPYHYQR 276 (430)
Q Consensus 214 ~rs~dg~~~l~~~~k~lPhvi~cRLwRWPDLqs~~eLk~l~~C~~~~~~~~~~vc~NPyhyes 276 (430)
+|++||+.++++ +++.||+++||+||||||++++|||++..|+++++.++++||+|||||+.
T Consensus 40 ~r~~dgrl~v~~-~k~~phvl~crlwRwpdL~~~~eLk~l~~C~~~~~~~~~~vC~NPyHy~r 101 (103)
T PF03165_consen 40 PRSLDGRLQVSG-RKGLPHVLYCRLWRWPDLRHSHELKRLPHCRFAFDSKNDEVCCNPYHYSR 101 (103)
T ss_dssp E--TTS-EEETT-EEE-HHHHHHHHHT-TT--SCCCEEE-TT-TT-GGG--SEEE--GGGEEE
T ss_pred cCccCccccccc-cccCceEEEEEEechhhcCCHHhcccCCCCCChhhcCCCCEEeCCcEeee
Confidence 356777766544 47899999999999999999999999999999998888899999999953
No 13
>cd00049 MH1 MH1 is a small DNA binding domain, binding in an unusal way involving a beta hairpin structure binding to the major groove. MH1 is present in Smad proteins, an important family of proteins involved in TGF-beta signalling and frequent targets of tumorigenic mutations. Also known as Domain A in dwarfin family proteins.
Probab=99.54 E-value=1.7e-15 Score=132.51 Aligned_cols=58 Identities=55% Similarity=1.257 Sum_probs=50.5
Q ss_pred CCCCccCCCCCCCCcccccccccCCCccCCCccccccccccCccCCCCccccCCCCCCC
Q psy13845 218 KGSTDLSNRSKGLPHVIYCRLWRWPSLQSHNELRSIDLCAFGFSLKRDQVCVNPYHYQR 276 (430)
Q Consensus 218 dg~~~l~~~~k~lPhvi~cRLwRWPDLqs~~eLk~l~~C~~~~~~~~~~vc~NPyhyes 276 (430)
|++.+++ .++++||++||||||||||++++||++++.|+++++++.++||+|||||+.
T Consensus 61 D~rl~~~-~r~~~phv~~crlwRWpDL~~~~eLk~l~~C~~~~~~~~~~vC~NPyHy~r 118 (121)
T cd00049 61 DGRLQVS-HRKGLPHVIYCRVWRWPDLRSNHELKRLETCEHAFDSKPDEVCINPYHYSR 118 (121)
T ss_pred ccccccc-ccCCCcceEEEeeeeccccCchHhheeCccCCCccccCCCeEEeCCceeee
Confidence 4444433 357899999999999999999999999999999998888999999999964
No 14
>PF03166 MH2: MH2 domain; InterPro: IPR001132 Mammalian dwarfins are phosphorylated in response to transforming growth factor beta and are implicated in control of cell growth []. The dwarfin family also includes the Drosophila protein MAD that is required for the function of decapentaplegic (DPP) and may play a role in DPP signalling. Drosophila Mad binds to DNA and directly mediates activation of vestigial by Dpp []. This domain is also found in nuclear factor I (NF-I) or CCAAT box-binding transcription factor (CTF). This entry represents the SMAD (Mothers against decapentaplegic (MAD) homologue) (also called MH2 for MAD homology 2) domain found at the carboxy terminus of MAD related proteins such as Smads. This domain is separated from the MH1 domain by a non-conserved linker region. The MH2 domain mediates interaction with a wide variety of proteins and provides specificity and selectivity to Smad function and also is critical for mediating interactions in Smad oligomers. Unlike MH1, MH2 does not bind DNA. The well-studied MH2 domain of Smad4 is composed of five alpha helices and three loops enclosing a beta sandwich. Smads are involved in the propagation of TGF-beta signals by direct association with the TGF-beta receptor kinase which phosphorylates the last two Ser of a conserved 'SSXS' motif located at the C terminus of MH2 [, , ].; GO: 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1MK2_A 1U7F_A 1MJS_A 1KHU_A 1DD1_C 1G88_A 1U7V_B 1MR1_B 1YGS_A 3DIT_B ....
Probab=99.52 E-value=4.6e-15 Score=138.44 Aligned_cols=74 Identities=45% Similarity=0.716 Sum_probs=59.0
Q ss_pred cccccccccCcccchhHhhhhccccCCceeeeecccCCCCCCceEeecccCCCCchhHHHhhhccCCceEEEee-cccc
Q psy13845 351 ERFCLGLLSNVNRNHVVEQIRRHIGKGPSISVDGFTDPSNSERFCLGLLSNVNRNHVVEQIRRHIGKGVRSLSV-AKEK 428 (430)
Q Consensus 351 ~rfCLg~lsnvnR~~~vE~tR~~IGkGvsL~vdGftDp~~~~~fcLg~l~n~~r~~~v~~tR~~iG~Gv~L~y~-~g~~ 428 (430)
+.||..+ |++.+++++|.+.++ +.++++|||+||++++|||||.|+|++|++.+++||+|||+||+|+|. +|+.
T Consensus 4 ~~Wc~I~-Y~E~~~rVG~~f~~~---~~~v~idG~~d~~~~~r~~Lg~~~n~~R~~~~~~~R~~IG~Gi~l~~~~~G~V 78 (181)
T PF03166_consen 4 EIWCSIA-YYELNTRVGEAFKAR---SPSVIIDGFTDPSDGDRFCLGQLSNVNRDSKTEKIRRHIGKGIKLSYEEDGNV 78 (181)
T ss_dssp SSSEEEE-EEETTEEESEEEEEE---SSEEEEESSSSSSSSSEEECTT---TT--HHHHHHHTTCTT-EEEEEETTTEE
T ss_pred CeeEEEE-EEecCCeEcceeEcc---CCeEEEeeccCCCCCCcEecCccCCCCCChHHhhHHheecCcEEEEEecCCeE
Confidence 4588765 556668888888653 679999999999999999999999999999999999999999999999 7764
No 15
>KOG3663|consensus
Probab=79.73 E-value=1.9 Score=45.33 Aligned_cols=82 Identities=24% Similarity=0.393 Sum_probs=46.7
Q ss_pred HHHHHHhhcc---CCHHHHHHHHhcCCCCccceEecCCCCCCCCcccCCCCCCCCceEeeeeecCC----------CCC-
Q psy13845 91 KSLVKKLKKS---NGLDELEKAITTQDPNTKCVTIPSARTDKGSTDLSNRSKGLPHVIYCRLWRWP----------SLQ- 156 (430)
Q Consensus 91 ~~l~Kklk~~---~~le~L~~Av~~~~~~t~Cv~i~~~r~~dgrl~~~~~~k~~Phv~~crl~Rwp----------dL~- 156 (430)
-.|+-||||. +.-|+++.+|+.. .+..||.-. -..+|+++-- ..|- =.=|+||-- -|.
T Consensus 73 SRLLaKlrKDIr~e~rEdFVltItGk-k~p~CVlSn--pDQKGKmRRI---DCLR--QADKVWRLDLVmVILFKgIPLES 144 (518)
T KOG3663|consen 73 SRLLAKLRKDIRPEYREDFVLTITGK-KPPCCVLSN--PDQKGKMRRI---DCLR--QADKVWRLDLVMVILFKGIPLES 144 (518)
T ss_pred HHHHHHHHhhcchHHHHHHHhhhcCC-CCCceeecC--ccccCceeeh---hhhh--hhchheeeeeeeEEeeccccccc
Confidence 3467777764 4467788887755 355687755 5667755310 0000 012455542 122
Q ss_pred -CCcccccccccccccCCCCCeeecCccchh
Q psy13845 157 -SHNELRSIDLCAFGFSLKRDQVCVNPYHYQ 186 (430)
Q Consensus 157 -~~~eLk~l~~C~~~~~~~~~~vC~NPyHy~ 186 (430)
....|..-+.|-++ ..||||||-.
T Consensus 145 TDGERL~ksp~C~hP------~LCVqPhHi~ 169 (518)
T KOG3663|consen 145 TDGERLEKSPQCSHP------GLCVQPHHIG 169 (518)
T ss_pred CchhhhhcCcccCCC------ccccccceee
Confidence 23455666677643 6999999964
No 16
>PF07624 PSD2: Protein of unknown function (DUF1585); InterPro: IPR011478 This entry represents a conserved region at the C terminus of a family of cytochrome-like proteins found in bacteria such as Rhodopirellula baltica and Solibacter usitatus. These proteins also contain IPR013036 from INTERPRO, IPR013039 from INTERPRO, IPR013042 from INTERPRO and IPR013043 from INTERPRO.
Probab=56.54 E-value=18 Score=29.01 Aligned_cols=48 Identities=25% Similarity=0.302 Sum_probs=39.6
Q ss_pred CChHHHHHHhhcccCCCCcchhHHHHHHHHHHhhcc-CCHHHHHHHHhc
Q psy13845 65 FTPPIVKKLLGWKKGDGEDKYSEKAVKSLVKKLKKS-NGLDELEKAITT 112 (430)
Q Consensus 65 ~~~~~v~~ll~~~~g~~~~~~~~ka~~~l~Kklk~~-~~le~L~~Av~~ 112 (430)
|....+++|+.+--|.+.+.--+.+|+.++.+++++ ..+.+|+.+|.+
T Consensus 23 ~~~~~~~kl~~YAlGR~~~~~D~~~i~~i~~~~~~~~y~~~~Li~~iv~ 71 (76)
T PF07624_consen 23 FARCFAEKLLTYALGRPLEFSDRCEIDRIVEAFKANGYRLRDLILAIVT 71 (76)
T ss_pred HHHHHHHHHHHHHcCCCCCcchHHHHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 445689999999999766666688999999999986 569999998864
No 17
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=50.47 E-value=33 Score=25.98 Aligned_cols=23 Identities=22% Similarity=0.394 Sum_probs=19.0
Q ss_pred EEEEEcC-eEEEEec-CCceeEeeC
Q psy13845 2 TLYYIGG-EVFAECL-SDSSIFVQS 24 (430)
Q Consensus 2 ~~~~~~~-~~~~~~~-~~~~~f~~s 24 (430)
+|.+.++ .+|++++ |..++||+.
T Consensus 24 ~i~~~~~~~~~i~d~~s~ngt~vng 48 (68)
T PF00498_consen 24 RISFDDDGQFYIEDLGSTNGTFVNG 48 (68)
T ss_dssp EEEEETTEEEEEEESSSSS-EEETT
T ss_pred EEEEeceeeEEEEeCCCCCcEEECC
Confidence 5788888 9999998 699999955
No 18
>KOG2884|consensus
Probab=39.17 E-value=63 Score=31.79 Aligned_cols=56 Identities=27% Similarity=0.353 Sum_probs=41.1
Q ss_pred HHHHHHhhcccCC-----------CCcchhHHHHHHHHHHhhccC----------------CHHHHHHHHhcCCCCccce
Q psy13845 68 PIVKKLLGWKKGD-----------GEDKYSEKAVKSLVKKLKKSN----------------GLDELEKAITTQDPNTKCV 120 (430)
Q Consensus 68 ~~v~~ll~~~~g~-----------~~~~~~~ka~~~l~Kklk~~~----------------~le~L~~Av~~~~~~t~Cv 120 (430)
.|.+--|.+||+. ..-+-.||..-.+.|+|||.+ -|++++.|+...+..+.||
T Consensus 92 ~iA~lalkhRqnk~~~~riVvFvGSpi~e~ekeLv~~akrlkk~~Vaidii~FGE~~~~~e~l~~fida~N~~~~gshlv 171 (259)
T KOG2884|consen 92 QIAQLALKHRQNKNQKQRIVVFVGSPIEESEKELVKLAKRLKKNKVAIDIINFGEAENNTEKLFEFIDALNGKGDGSHLV 171 (259)
T ss_pred HHHHHHHHhhcCCCcceEEEEEecCcchhhHHHHHHHHHHHHhcCeeEEEEEeccccccHHHHHHHHHHhcCCCCCceEE
Confidence 6777788888852 123335778888999999732 2567777887777888999
Q ss_pred Eec
Q psy13845 121 TIP 123 (430)
Q Consensus 121 ~i~ 123 (430)
++|
T Consensus 172 ~Vp 174 (259)
T KOG2884|consen 172 SVP 174 (259)
T ss_pred EeC
Confidence 999
No 19
>PHA00008 J DNA packaging protein
Probab=38.82 E-value=21 Score=23.12 Aligned_cols=13 Identities=31% Similarity=0.414 Sum_probs=11.1
Q ss_pred CceEEEeeccccc
Q psy13845 417 KGVRSLSVAKEKL 429 (430)
Q Consensus 417 ~Gv~L~y~~g~~~ 429 (430)
||-+|.||||...
T Consensus 13 KGARLWYVGGtQf 25 (26)
T PHA00008 13 KGARLWYVGGTQF 25 (26)
T ss_pred CceEEEEeccEEc
Confidence 7999999999753
No 20
>PF10401 IRF-3: Interferon-regulatory factor 3; InterPro: IPR019471 This is the interferon-regulatory factor 3 chain of the hetero-dimeric structure which also contains the shorter chain CREB-binding protein. These two subunits make up the DRAF1 (double-stranded RNA-activated factor 1). Viral dsRNA produced during viral transcription or replication leads to the activation of DRAF1. The DNA-binding specificity of DRAF1 correlates with transcriptional induction of ISG (interferon-alpha, beta-stimulated gene). IRF-3 pre-exists in the cytoplasm of uninfected cells and translocates to the nucleus following viral infection. Translocation of IRF-3 is accompanied by an increase in serine and threonine phosphorylation, and association with the CREB coactivator occurs only after infection. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1J2F_A 1QWT_A 3A77_B 1ZOQ_A 3DSH_A.
Probab=33.12 E-value=86 Score=29.03 Aligned_cols=45 Identities=16% Similarity=0.284 Sum_probs=30.4
Q ss_pred CEEEEEcCeEEEEecCCceeEeeCCccccccCcCcceeeecCCCCceeEE
Q psy13845 1 MTLYYIGGEVFAECLSDSSIFVQSPNCNQRYGWHPATVCKIPPVKRKTIS 50 (430)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~f~~s~~~~~~~~~~~~~~~k~~~~~~~~~~ 50 (430)
|.|...++.+||.+++..-||...+...... .|+ |++.+...+|-
T Consensus 76 l~L~~~~~gI~akRlc~~~Vfw~g~~~~~~~--~P~---kL~r~~~~~lF 120 (180)
T PF10401_consen 76 LLLWSNPQGIYAKRLCQCRVFWSGPEAPPSD--EPN---KLEREEPVKLF 120 (180)
T ss_dssp EEEEEETTEEEEEE-SSS-EEEECCTSS-S---S-S---E--CTS-EEEE
T ss_pred EEEEEeCCEEEEEecCCceEEEEcCCccCCC--CCc---ccCcCCceeec
Confidence 4577889999999999999999999886655 454 88888777663
No 21
>PF04726 Microvir_J: Microvirus J protein; InterPro: IPR006815 This small protein is involved in DNA packaging, interacting with DNA via its hydrophobic C terminus. In bacteriophage phi-X174, J is present in 60 copies, and forms an S-shaped polypeptide chain without any secondary structure. It is thought to interact with DNA through simple charge interactions [].; GO: 0003677 DNA binding, 0019073 viral DNA genome packaging, 0019028 viral capsid; PDB: 1M06_J 1GFF_3 1RB8_J 2BPA_3.
Probab=30.34 E-value=19 Score=22.84 Aligned_cols=12 Identities=33% Similarity=0.393 Sum_probs=5.5
Q ss_pred CceEEEeecccc
Q psy13845 417 KGVRSLSVAKEK 428 (430)
Q Consensus 417 ~Gv~L~y~~g~~ 428 (430)
||-+|.||||..
T Consensus 12 kgarlwyvgg~q 23 (24)
T PF04726_consen 12 KGARLWYVGGTQ 23 (24)
T ss_dssp SSS----SSS--
T ss_pred CceEEEEeccee
Confidence 799999999964
No 22
>PF10709 DUF2511: Protein of unknown function (DUF2511); InterPro: IPR019648 This entry is represented by Bacteriophage PsP3, Gp28. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=26.44 E-value=69 Score=26.91 Aligned_cols=27 Identities=30% Similarity=0.602 Sum_probs=22.0
Q ss_pred EEcCeEEEEecCCceeEeeCCcccccc
Q psy13845 5 YIGGEVFAECLSDSSIFVQSPNCNQRY 31 (430)
Q Consensus 5 ~~~~~~~~~~~~~~~~f~~s~~~~~~~ 31 (430)
|-..||.++|..+.++||=.++..+++
T Consensus 13 ft~eev~l~C~~~~alfv~n~~tl~qY 39 (87)
T PF10709_consen 13 FTVEEVMLECRPGNALFVINPSTLMQY 39 (87)
T ss_pred ceeeeEEEEEcCCCEEEEEcCCCCccc
Confidence 345799999999999999887775554
No 23
>smart00240 FHA Forkhead associated domain. Found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain.
Probab=24.32 E-value=88 Score=22.03 Aligned_cols=23 Identities=26% Similarity=0.475 Sum_probs=18.8
Q ss_pred EEEEEcCe-EEEEecC-CceeEeeC
Q psy13845 2 TLYYIGGE-VFAECLS-DSSIFVQS 24 (430)
Q Consensus 2 ~~~~~~~~-~~~~~~~-~~~~f~~s 24 (430)
+|++..+. +|+++++ ..++||+.
T Consensus 25 ~i~~~~~~~~~i~d~~s~~gt~vng 49 (52)
T smart00240 25 EIVYDGGGRFYLIDLGSTNGTFVNG 49 (52)
T ss_pred EEEECCCCeEEEEECCCCCCeeECC
Confidence 56777765 9999999 88999875
Done!