Query 000683
Match_columns 1353
No_of_seqs 194 out of 243
Neff 5.5
Searched_HMMs 46136
Date Mon Apr 1 21:53:55 2013
Command hhsearch -i /work/01045/syshi/lefta3m/000683.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/leftcdd/000683hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5103 CDC39 Cell division co 100.0 4E-143 9E-148 1281.9 51.8 1030 6-1353 25-1092(2005)
2 KOG1831 Negative regulator of 100.0 4E-120 8E-125 1108.6 28.6 577 532-1353 82-665 (1591)
3 smart00543 MIF4G Middle domain 93.2 0.84 1.8E-05 49.0 11.8 181 972-1162 2-196 (200)
4 KOG1831 Negative regulator of 85.9 91 0.002 43.2 22.7 124 1010-1146 658-782 (1591)
5 PF02854 MIF4G: MIF4G domain; 84.7 2.9 6.3E-05 44.7 7.7 109 972-1081 2-117 (209)
6 PF02847 MA3: MA3 domain; Int 58.8 78 0.0017 31.2 9.9 71 686-765 17-87 (113)
7 COG5088 SOH1 Rad5p-binding pro 58.1 23 0.00051 35.1 5.6 89 984-1077 15-108 (114)
8 PF08542 Rep_fac_C: Replicatio 40.0 90 0.0019 29.6 6.6 60 8-70 4-63 (89)
9 smart00544 MA3 Domain in DAP-5 34.7 2E+02 0.0044 28.4 8.5 71 686-765 17-87 (113)
10 KOG3769 Ribonuclease III domai 33.5 92 0.002 36.8 6.4 50 121-170 111-160 (333)
11 KOG2140 Uncharacterized conser 26.3 1.4E+02 0.0031 37.7 6.7 172 968-1162 162-344 (739)
12 PF08514 STAG: STAG domain ; 22.2 41 0.00089 34.4 1.1 61 1007-1088 5-65 (118)
13 PF01603 B56: Protein phosphat 21.3 1.1E+03 0.025 29.1 13.3 109 610-719 43-163 (409)
14 PF12054 DUF3535: Domain of un 20.4 3.8E+02 0.0083 33.6 9.0 109 659-785 229-343 (441)
15 PRK00218 putative lysogenizati 20.1 2.5E+02 0.0053 31.8 6.5 90 705-815 32-134 (207)
No 1
>COG5103 CDC39 Cell division control protein, negative regulator of transcription [Cell division and chromosome partitioning / Transcription]
Probab=100.00 E-value=4.1e-143 Score=1281.88 Aligned_cols=1030 Identities=27% Similarity=0.416 Sum_probs=768.8
Q ss_pred CCcHHHHHHHHHhhhhhchHHHHHHHHHHHh-hccchhhHHHHhhhhhcccCC-CCCCChh---hHHHHHHHHHHhhcCC
Q 000683 6 STVPSQIRFLLQSLNEANADSVFRELCQFIE-YGIEGSTMMLQTCMDHLNLHG-TGLKNPQ---LESVVASVFKYIMDKP 80 (1353)
Q Consensus 6 ~~~~~qI~~Lv~~l~kkn~~~~~~el~qlv~-~G~ea~~~lLr~~l~~~~~~~-~~~k~~~---~~~LL~~~~~~ll~kp 80 (1353)
+.+-+||.+|++.|+..||++.-+||.|+++ ...+-.++++|.++.-..++- +.+|... --++|-+||+.++.|-
T Consensus 25 sIV~AQI~fLlsTL~eDqydt~~eqIRqlinkna~~vY~~~~rRLiq~nS~~If~tGK~~~~~a~~~~LL~Elks~~~Kr 104 (2005)
T COG5103 25 SIVKAQILFLLSTLREDQYDTKLEQIRQLINKNAPRVYHHFLRRLIQGNSYRIFGTGKSSDGLATYKLLLDELKSLTKKR 104 (2005)
T ss_pred HHHHHHHHHHHHHhhccchhHHHHHHHHHHccCCcHHHHHHHHHHhcccchhhhccCcccchhHHHHHHHHHHHhhhhhh
Confidence 4577899999999999999999999999998 999999999999994432211 1344433 4588999999999865
Q ss_pred CccchhhhcccCC--cCCHHHHHHHHhhcCCCchhhhhhhhhhccCCChHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHH
Q 000683 81 NFSTVFSQSVKIT--EINEQLLENLSDVLNLSLPERIGIGLALSDSENLDALMCGKNFCMAQIERLCANPVPMNSAEQIQ 158 (1353)
Q Consensus 81 ~f~T~lc~A~~~~--~~~~~fl~~ls~~L~Ls~~qev~~gLAL~~S~n~e~r~~a~~f~~~~i~el~~n~~~~~s~e~lh 158 (1353)
. ..|+.+. +.=++|-=+++ +||.++ .++...-.+. |...+.+-
T Consensus 105 ~-----sD~Is~~dsevFed~~FQ~s------------iGlT~S-------------Ll~n~Fqs~~-Nq~~~~t~---- 149 (2005)
T COG5103 105 F-----SDAISGSDSEVFEDFHFQFS------------IGLTTS-------------LLKNTFQSLL-NQLSDPTQ---- 149 (2005)
T ss_pred h-----hhHhhcchhhhhcchhhhhh------------hhhhHH-------------HHHHHHHHHH-hhccchHh----
Confidence 4 5666654 22223322222 444443 2233222222 11111000
Q ss_pred HHHHHHhhccchhHhHHHHHHHHhhhcCCCCCCccccCCCCCCCccccccccccccccCCCCchHH-----HHHh-hhcc
Q 000683 159 NIIMFLQRSSDLSKHVDSLMQILSLLQSKDHTQFVLNPVLPDELHDATSLRDLDLFHECRDDDFDD-----ILAE-MEKE 232 (1353)
Q Consensus 159 ~il~~l~~~~gls~~~~~f~~~l~~~~p~e~~p~~laPll~~~~~~~~~~r~~~~~~~~~~~~~~~-----~~~~-~~~~ 232 (1353)
++.....++|+..++ ..|.++ .+.+ ++++
T Consensus 150 --------------------------------------------qqS~d~NDld~lr~~-~Tdydr~~f~q~i~~~Le~s 184 (2005)
T COG5103 150 --------------------------------------------QQSIDKNDLDLLREG-TTDYDRKIFRQEIKDVLEKS 184 (2005)
T ss_pred --------------------------------------------hhhcccchHHHHhcC-CchHHHHHHHHHhHHHHHcC
Confidence 000000111111111 001111 1111 0111
Q ss_pred CcHHHHHHhhCcccccCHHHH----HHHHhcCCCCCHHHHHHHHHHHHhhccCCccCccchhhHHhhccCCCCCCCCCCC
Q 000683 233 MSMGDVMNELGYGCSADASQC----KEILSLFTPLTEITLSRILGAIARTHAGLEDNQNTFSTFTLALGCSTMSDLPPLS 308 (1353)
Q Consensus 233 ~sl~~~i~elG~~~t~s~~~c----~~~L~~~~~l~e~~va~vlg~ma~t~sgl~d~~~~~~~~~~~~g~~~~~~~~~~~ 308 (1353)
..+ ... .|++ -++.+.. .++|+-.+.-.+.||||.+-.|+.-| ..+
T Consensus 185 ~~~--~~~-~~p~-e~~~~~l~~~l~~Il~P~~~~~~~dvar~il~~~~~~--------------------------D~~ 234 (2005)
T COG5103 185 DPL--TAL-FGPR-EVDRSFLDDALQRILRPRREVVPEDVARAILFMADFP--------------------------DRG 234 (2005)
T ss_pred Cch--hhh-cCcc-hhhHHHHHHHHHHHhCCCccCCcchHHHHHhhhhhcc--------------------------ccc
Confidence 000 000 0110 1122222 23344334577888886665555332 235
Q ss_pred CCCHHHHHHHHHhhCCCCCHHHHHhhcCCCCCCcCChhhHHHHHHHHhh-hcCCCccccccccccccCchh-hhHHHHHH
Q 000683 309 SWNVDVLVKAIKQLAPNTNWIRVVENLDYEGFYIPTEEAFSFFMSVYKY-ACQEPFPLHAVCGSVWKNTEG-QLSFLRYA 386 (1353)
Q Consensus 309 tWn~~v~v~alk~~~p~lnW~~Vi~~lD~~~f~i~d~~~l~ll~~~~~~-~~~~~Fpi~~l~~~~W~N~~~-QlSfl~~~ 386 (1353)
.||.-..+.+++..+..+||.+|+.+||.+.|.|+.......++.+|-. +.+.+||.+.+|. .|||... |+++.-|.
T Consensus 235 ~w~~v~~~~a~~s~~e~iNW~~v~s~f~~~~F~i~~l~p~~v~~~c~f~~~~~~~v~~eff~~-~Wkn~~~~~l~i~lhi 313 (2005)
T COG5103 235 EWNLVAIVGAMKSNLEEINWRDVYSCFLDVNFSIWTLEPLYVIIDCWFYISGIITVPYEFFFK-RWKNERAQILFIRLHI 313 (2005)
T ss_pred ccchHHHHHHHHhhhhhcCHHHHHHHhcCcceeeccCcchHHHHHHHHHHhcCCCccHHHHHH-HhcchhhhhHhhheee
Confidence 6999999999999999999999999999999999977666666555554 5567999999994 8999999 55555566
Q ss_pred hhCCCCccccCcC-ccccccccCCCCccccc-cccccccchHHHHHHHHHhhhcCchHHHHHHhhhhhhhChhHHHHHHh
Q 000683 387 VASPPEVFTFAHS-ARQLPYVDAVPGLKLQS-GQANHAWLCLDLLDVLCQLSEMGHASFARSMLEYPLKQCPEMLLLGMA 464 (1353)
Q Consensus 387 l~~pp~~f~f~~~-~rk~v~~d~~~~~~~~~-~~~~~~W~sldLve~L~~Lae~~~~~~vr~l~e~p~k~cpellllgl~ 464 (1353)
.+.+...|+...- +.+.|..+...+.+... ....+++||.+|++++ .+++.....-..++| +...||++.+||.
T Consensus 314 ~s~~~~~fd~~Nv~~tr~Vs~~~~~~~~~~ny~~~~snlNc~el~Q~~-~l~~~p~i~y~~~lF---lN~~pE~~~a~L~ 389 (2005)
T COG5103 314 ESDEKRTFDYSNVFFTRIVSIEDSRGHRFKNYMGYESNLNCVELFQCI-MLGSLPLIEYIARLF---LNKSPEWCAAGLG 389 (2005)
T ss_pred eecccchheecccceeEEEeeecCchHHHHHHHHHhcccCHHHHHHHH-HhccchHHHHHHHHH---hccCHHHHHHHHH
Confidence 6666667877443 44555544433333222 4478999999999999 344333222233466 7889999999996
Q ss_pred hc-----CCcchHHHHHHHHHhhHHHhc-CCCcHHHHHHHHhhChhhHHHHHHHhhhcCCchHHHHHHHHHHhhhhhhhh
Q 000683 465 HI-----NTAYNLIQYEVSFAVFPMIIK-STMSNGMILHIWHVNPNIVLRGFVDAQNMEPDCTIRILEICQELKILSSVL 538 (1353)
Q Consensus 465 qi-----~~~~~~l~~ell~~lf~~fl~-~~~~~~vi~~lW~~~~~~v~~~l~d~y~~d~~~l~rIldvaqelk~L~~ll 538 (1353)
.+ +-.||+.+.+.+...+-+++. ..++++|+..+...+|+.++++..-...+|...++|++|+.-|+|.|+.+.
T Consensus 390 ~~~~~f~~L~~N~v~~s~if~~ll~~f~n~~p~sFvfv~~~rT~p~~~~~~~r~v~~kd~~pv~~~l~~~le~~~l~~V~ 469 (2005)
T COG5103 390 FVQPKFSPLAWNPVQESRIFEELLMGFANGAPNSFVFVVLFRTHPEMMLQKSRLVLAKDGIPVSRLLDIFLEHKMLPLVS 469 (2005)
T ss_pred HhhhhhhhhhcCchHHHHHHHHHHHHHhcCCCCceEEEEEEecCHHHHHHHHHHHHhcCCCcHHHHHHHHHhcCchhhhh
Confidence 65 447999999988888888886 568889999999999999999998888999999999999999999999999
Q ss_pred ccCCchhHHHHHHHhhcccccCHHHHHHHHhhcCcc-h----HHHHHHHHHHHHhccccccccCCCCCCCccccccccch
Q 000683 539 EMIPSPFAIRLAVIASQKELVDLEKWLSINLSTYKD-V----FFEECLKFVKEVQFGRSQDFSAQPFHHSGALLNLYMEK 613 (1353)
Q Consensus 539 ~~~p~~f~idLA~lAsrre~l~LekWL~~~l~~~~~-~----F~~a~l~FL~~k~~~~~~~~~~~~~~~~~~~~~L~~et 613 (1353)
|..|..|++|+++|++.|+.++|..|+..++....+ + |+...++||+.|+.......+.+ ..+.+ ++..|
T Consensus 470 n~lP~~f~~~i~vL~~aR~~l~~~~Wl~~~~~~~~dad~~NVfvv~~~~~l~sk~s~~k~p~~q~---ee~~~--f~~~t 544 (2005)
T COG5103 470 NLLPPEFCFDIIVLSSARDHLNLGIWLSNNLTTRKDADGLNVFVVSLVQYLDSKVSKHKEPEKQK---EESVM--FPLNT 544 (2005)
T ss_pred hcCCHHHHHHHHHHHHHHHhcchhhhcccCceeeecCCcccchHHHHHHHHHHHHhhcCChhhhc---cccee--eehhh
Confidence 999999999999999999999999999999987665 3 99999999999997643211111 11122 33355
Q ss_pred HHHHHHHHHhhcCCCCchHHHHHHHHHHHHhhccCCCccCCC-CCCCC-----CCCCCchhHHHHHHHHHHHhhccccCH
Q 000683 614 IPVILKLLKAHIGLITSTKLSEEIEKFQAVVLDSTPRLQNGE-AADSS-----TSEGYADDIEAEANSYFHQMFSGQLTI 687 (1353)
Q Consensus 614 ~~~ll~~L~~~~~~~~s~~~~e~l~~~~~~~~~~~prL~n~~-~~d~~-----~~~~~~~dVE~Ean~yfqkmY~~eisI 687 (1353)
+-.+|..+..... +-.+.++.++..|++.||||++.| ++|+. +.++++.|||+||.+|||+||+++++|
T Consensus 545 vieil~t~~~~V~-----q~~~~~k~~~~~~l~~fprli~~G~~~Ds~v~at~tt~s~~~dIE~E~~sy~q~~y~~~~~I 619 (2005)
T COG5103 545 VIEILGTFTKAVE-----QYIRILKPETVVVLNEFPRLIPHGLRRDSIVAATNTTRSKEIDIEEEASSYIQQIYNSQRGI 619 (2005)
T ss_pred HHHHHHHhHHHHH-----HHHHhcCcceEehHhhhhhhccCCCCcchhhhccCcccccCccHHHHHHHHHHHHHHhcccH
Confidence 5444444433221 225778888889999999999998 66652 346899999999999999999999999
Q ss_pred HHHHHHHHHhhcCCcccchhhHHHHHHhHHhhhccCCCCcHHHHHHHHHHHHHHhhhhccchhhHHHHHHHHHHHhcCCC
Q 000683 688 EAMVQMLARFKESSVKREHSIFECMIGNLFEEYRFFPKYPERQLRIAAVLFGSIIKHQLVTHLTLGIALRGVLDALRKPA 767 (1353)
Q Consensus 688 ~~ii~~L~~~k~S~~~reqdvFaCMIh~LFdEYrff~~YP~~eL~iTA~LFG~lI~~~Lv~~~~L~iALr~ILeAlr~p~ 767 (1353)
+++|+.||+|++|++|||+|+|+|+-|.|||||+||++||.++|++|||||||||+++|+++.+|++|+|||..+++.|+
T Consensus 620 ~~~I~~l~~f~~senprd~elfsci~hal~~ey~ff~dyPl~ALaltavLfGslI~f~ll~~~~L~vA~ryI~~~lk~P~ 699 (2005)
T COG5103 620 ESSINQLKEFLRSENPRDKELFSCIFHALLEEYGFFYDYPLSALALTAVLFGSLIKFRLLPKPYLRVAIRYIKGSLKHPE 699 (2005)
T ss_pred HHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHhcccccCcchHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHhcCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccccHHHHHHHHHHHhhhhhhHHHHHHhcccccccccHHHHHHHHHHHHhhhcCCCCCCCCCCCcccccccccccCCC
Q 000683 768 DSKMFVFGTKALEQFVDRLIEWPQYCNHILQISHLRSTHAELVAFIERALARISSGHLESDGASNPAAHQHVSSQATSGN 847 (1353)
Q Consensus 768 ~skmf~FGi~AL~qF~~RL~ewPqyC~~Ll~ip~L~~~~p~l~~~ie~~~~~~~~~~~~~~~~~~~~~~q~~~~q~~~~~ 847 (1353)
+||||+||+|||++|+.||++||+||+.++.||.|+. .+++|+.|-++.. ..+. .+
T Consensus 700 ~skmf~Fg~qal~~Fq~kLp~Yp~yc~~vl~ip~l~~-r~~iy~sivem~s----~eNt-------~~------------ 755 (2005)
T COG5103 700 NSKMFSFGFQALEVFQEKLPSYPSYCSEVLEIPTLNN-RILIYKSIVEMDS----NENT-------EV------------ 755 (2005)
T ss_pred chhhHHHHHHHHHHHHHhhhhhhHHHHHHhccccccc-chHHHHHHHHHHh----ccCC-------cc------------
Confidence 9999999999999999999999999999999999965 8999998866531 1100 00
Q ss_pred CcccCCCcccccchhhhhHHhhhhccccccccccccccccCCCCCCcccCCCCCccCCCCCCcchhhhcccCCCcccccc
Q 000683 848 GEVSGSGITQLGQQLSSQIQLQQRSESVVDDRHKVSAASSSDMKPLLSSIGQPSSVAPLGDTSSAQKLHNAVSAPAMLSI 927 (1353)
Q Consensus 848 ~~~~~~~~~~~~~q~~~~~~~qq~~~~~l~~~~~~s~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~ 927 (1353)
++ +++..|.. |.
T Consensus 756 ------------------------------Ek-------a~p~~pm~-----------------pl-------------- 767 (2005)
T COG5103 756 ------------------------------EK-------ANPTHPML-----------------PL-------------- 767 (2005)
T ss_pred ------------------------------cc-------cCCCCccc-----------------ch--------------
Confidence 00 00000000 00
Q ss_pred CCCccCCCCCccccccccccchhhHHHHhhcCCCCCCCCChhhhhhhhhhhhcCCcccHHHHHHHHHHHhhhcchhhhhH
Q 000683 928 SSGFARPSRGVTSTKFGSALNIETLVAAAERRETPIEAPASEVQDKISFIINNISALNVEAKAKEFTEILKEQYYPWFAQ 1007 (1353)
Q Consensus 928 ~~~~~~~~~~~~~~~~~~a~nidtl~~~~e~~~~~i~~P~e~vqdKI~FiiNNls~~Nl~~K~~El~~~L~~~y~~WFA~ 1007 (1353)
.-|++ +.+. -+...|.-++++.++|+|.+||++..|+..|++|+|+-|++.|.+||+.
T Consensus 768 -~~fv~-------------~~v~--------c~~n~Eg~~~evV~~iLFaiNNl~~ln~n~ki~~lk~~Ltp~y~~wfs~ 825 (2005)
T COG5103 768 -EDFVR-------------LIVK--------CDANNEGRATEVVKSILFAINNLLDLNRNDKIHRLKEALTPGYVGWFSI 825 (2005)
T ss_pred -hhhhe-------------eEec--------cccCccccHHHHHHHHHHHhhhHHhhhccchHHHHHHhcCcccccceee
Confidence 00110 0000 1112334456777779999999999999999999999999999999999
Q ss_pred HHHHhhcccCCchhHHHHHHHHHhCChhHHHHHHHHHHHHHHHHhcccccccChHHHHHHHHhHHhhhhhhhhcCccccc
Q 000683 1008 YMVMKRASIEPNFHDLYLKFLDKVNSKALNREIVQATYENCKVLLGSELIKSSSEERSLLKNLGSWLGKLTIGRNQVLRA 1087 (1353)
Q Consensus 1008 YLV~kRas~EpN~H~LY~~fld~l~~~~L~~~vl~~Ty~~i~~LL~se~~~~~s~eRslLKNLG~WLG~iTLarNkPI~~ 1087 (1353)
|||.+|++.|||||+||.++++.++++.||+.+.+.|.+.++.||+...- +.+|+++|||||+|||+|||||||||+|
T Consensus 826 y~vtqR~~~e~n~~~ly~kvve~lgS~dly~~~~r~TL~~l~~ll~~~~e--s~~ekk~lKnLgswLG~ItLa~NkpIt~ 903 (2005)
T COG5103 826 YMVTQRSTAEENCRRLYGKVVERLGSKDLYLRFSRKTLEFLKMLLDYRCE--SPSEKKVLKNLGSWLGRITLAKNKPITS 903 (2005)
T ss_pred EEEEeeccccchHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHhcccc--ChHHHHHHHHHHHHHhHHHHhhcCcccc
Confidence 99999999999999999999999999999999999999999999986533 8899999999999999999999999999
Q ss_pred CCCChhHHHHHHHhcCceeEEechhhhhccccCCCccccCCCccHHHHHHHHHHHhcCCccchhhHHHHHHHHhhcCCCc
Q 000683 1088 REIDPKSLIIEAYEKGLMIAVIPFTSKILEPCQSSLAYQPPNPWTMAILGLLAEIYSMPNLKMNLKFDIEVLFKNLGVDM 1167 (1353)
Q Consensus 1088 k~ld~K~LL~eaY~~g~L~~ViPFV~KVLe~~~~S~vFkPPNPW~m~IL~lL~Ely~~~~LKlnLKFEIEvL~K~L~ld~ 1167 (1353)
+++|||++|+|||+.||+..|||||||||++++.|+||||||||+||||+||.|||+++++|++||||||+|+|+|++++
T Consensus 904 ~q~~Fk~~lve~~~~~Ri~~vvpFV~k~L~~as~s~IFkPpNPW~mgILkLL~El~~~a~~~l~lkFEie~Ll~~lnv~~ 983 (2005)
T COG5103 904 EQFDFKKFLVESVECRRILFVVPFVSKFLRQASCSIIFKPPNPWVMGILKLLSELHSCAPRVLRLKFEIEGLLRHLNVEL 983 (2005)
T ss_pred ccccHHHHHHHHhhcCceEEeehHHHHHHHhcccceEecCCCchHHHHHHHHHHHHhcCcceeehhhhHHHHHHhcceee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccccccchhhhhcCCCCCCCCccCCCCCCccCCCCccccCCCCCCCCCCccCCCCCCCCCcccccccccccccCcC
Q 000683 1168 KDITPTSLLKDRKREIEGNPDFSNKDVGASQPQLVPEVKPAIVSPLGHVDLPLDVASPPNSGGPTHLLSQYAAPLRLSSG 1247 (1353)
Q Consensus 1168 ~di~ps~~L~~r~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~ 1247 (1353)
+.|||+..++++.-.-. +.. +..||. + .+ +++|.+ +..++||.....
T Consensus 984 ~~ikPs~~~~n~~V~ks--------~LE----ke~~Ed----v--L~-a~~~d~----------~~~~~qyi~~~s---- 1030 (2005)
T COG5103 984 VPIKPSKSLGNHLVLKS--------RLE----KELPED----V--LN-AKFPDG----------TDYLAQYIIEDS---- 1030 (2005)
T ss_pred ccCChhhhhCcHHHHHH--------HHh----hhchHH----H--Hh-hhcccc----------chHHHHHHHHhh----
Confidence 99999999987653110 000 011110 0 00 011100 113344442100
Q ss_pred cchhhHHHhhccCCCCCCcccccccccCCCCCCCcccccCCCCCCCceEEecCcchhcccchhhhhHHHHHHHHhHHhhh
Q 000683 1248 TLMEDEKLAALGISDQLPSAQGLFQASQSQSPFSVSQLSTPIPNIGTHVIINQKLTALGLHLHFQRVVPIAMDRAIKEIV 1327 (1353)
Q Consensus 1248 ~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~s~~~i~~~i~~l~~~v~in~~l~~~~~~p~lk~iv~~AierAIrEII 1327 (1353)
+ .....| +...+...| -|.+|++.++|++.+||||+
T Consensus 1031 ----------------------------S--q~TvtD-------~va~~~g~P-------~PaiK~~~Qlal~~SVrEI~ 1066 (2005)
T COG5103 1031 ----------------------------S--QITVTD-------LVARHVGSP-------KPAIKNLTQLALDLSVREIC 1066 (2005)
T ss_pred ----------------------------h--cchHHH-------HHHHHcCCC-------ChHHHHHHHHHHHHHHHHHH
Confidence 0 011111 111111122 29999999999999999999
Q ss_pred hhhhhhhhHHHHHHHHHHHhhcccCC
Q 000683 1328 SGIVQRSVSIATQTTKELVLKVCFLS 1353 (1353)
Q Consensus 1328 ~PVVeRSVtIA~iTT~elV~KDFA~d 1353 (1353)
+-|||||+.||++||..|++|||||.
T Consensus 1067 ~aVVeks~gIAi~Tt~~l~~KDFa~e 1092 (2005)
T COG5103 1067 GAVVEKSCGIAIQTTMALFKKDFAME 1092 (2005)
T ss_pred HHHHHHhccchhhHHHHHHHHHhhhc
Confidence 99999999999999999999999984
No 2
>KOG1831 consensus Negative regulator of transcription [Transcription]
Probab=100.00 E-value=3.6e-120 Score=1108.62 Aligned_cols=577 Identities=35% Similarity=0.550 Sum_probs=448.3
Q ss_pred hhhhhhhccCCchhHHHHHHHhhcccccCHHHHHHHHhhcCcchHHHHHHHHHHHHhccccccccCCCCCCCcccccccc
Q 000683 532 KILSSVLEMIPSPFAIRLAVIASQKELVDLEKWLSINLSTYKDVFFEECLKFVKEVQFGRSQDFSAQPFHHSGALLNLYM 611 (1353)
Q Consensus 532 k~L~~ll~~~p~~f~idLA~lAsrre~l~LekWL~~~l~~~~~~F~~a~l~FL~~k~~~~~~~~~~~~~~~~~~~~~L~~ 611 (1353)
.-++-|.|+.||.++++.+.+|+.++++++..||.+++.--.+ |..++.-.+.. +..++.+..+...
T Consensus 82 ~~~~~v~Nm~pn~~~~n~~~la~~~~a~~F~~~l~~~~~~~~~-----~~~~~s~~~~~--------~q~~~~~~~~~~~ 148 (1591)
T KOG1831|consen 82 PGMDIVGNMSPNLEALNIRDLASCFGAVNFSIWLLESLYLMID-----DAVPLSLIITA--------PQEPSFKPWPNER 148 (1591)
T ss_pred CcchhhhhcCcchhhhchHhhhhhcCCCCchhhhcccceeecc-----CCCcccceeec--------cccccCCCChhHH
Confidence 4578889999999999999999999999999999988653211 11111111110 0011111111100
Q ss_pred -chHHHHHHHHHhhcCCCCchHHHHHHHHHHHHhhccCCCccCCCCCCC-----CCCCCCchhHHHHHHHHHHHhhcccc
Q 000683 612 -EKIPVILKLLKAHIGLITSTKLSEEIEKFQAVVLDSTPRLQNGEAADS-----STSEGYADDIEAEANSYFHQMFSGQL 685 (1353)
Q Consensus 612 -et~~~ll~~L~~~~~~~~s~~~~e~l~~~~~~~~~~~prL~n~~~~d~-----~~~~~~~~dVE~Ean~yfqkmY~~ei 685 (1353)
.++..++-.... + ++..+...++|.+|. ....+|++|||+|||+||||||+ .+
T Consensus 149 ~~qi~~l~p~~~~---------------q-----~qrt~s~sa~~~~d~v~~~~~~~~~~s~die~E~~sYfqkiYn-~l 207 (1591)
T KOG1831|consen 149 FAQIYFLLPIGPS---------------Q-----LQRTESVSAPGPHDPVFFARQVSIEFSRDIEFEVNSYFQKIYN-CL 207 (1591)
T ss_pred HHHHHHHccCChh---------------h-----ccccccccCCCCCCchhhhcccccccChhHHHHHHHHHHHHHH-Hh
Confidence 111111110000 0 011122224444554 23468999999999999999999 99
Q ss_pred CHHHHHHHHHHhhcCCcccchhhHHHHHHhHHhhhccCCCCcHHHHHHHHHHHHHHhhhhccchhhHHHHHHHHHHHhcC
Q 000683 686 TIEAMVQMLARFKESSVKREHSIFECMIGNLFEEYRFFPKYPERQLRIAAVLFGSIIKHQLVTHLTLGIALRGVLDALRK 765 (1353)
Q Consensus 686 sI~~ii~~L~~~k~S~~~reqdvFaCMIh~LFdEYrff~~YP~~eL~iTA~LFG~lI~~~Lv~~~~L~iALr~ILeAlr~ 765 (1353)
+|+++|++|+|||.|.++|||+||+||.|+||||||||++||++||++||+||||||.|+|+++.+||+|+|+|++|++.
T Consensus 208 sI~~vI~lL~rfr~Se~~Rdq~vf~C~~~~lF~EyrFF~dYPe~~L~~Ta~lfGsiI~~~Lls~v~l~la~R~Vl~~l~~ 287 (1591)
T KOG1831|consen 208 SIFQVIDLLQRFRLSELPRDQEVFACAAHNLFEEYRFFRDYPELALATTAVLFGSIIFFVLLSFVELGLALRLVLAALGI 287 (1591)
T ss_pred hHHHHHHHHHhcccccChhhhhHHHHHHhhccccccccccCHHHHHHHHHHhcchhHHHHHHhhhHHHHHHHHHHHHhcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccccHHHHHHHHHHHhhhhhhHHHHHHhcccccccccHHHHHHHHHHHHhhhcCCCCCCCCCCCcccccccccccC
Q 000683 766 PADSKMFVFGTKALEQFVDRLIEWPQYCNHILQISHLRSTHAELVAFIERALARISSGHLESDGASNPAAHQHVSSQATS 845 (1353)
Q Consensus 766 p~~skmf~FGi~AL~qF~~RL~ewPqyC~~Ll~ip~L~~~~p~l~~~ie~~~~~~~~~~~~~~~~~~~~~~q~~~~q~~~ 845 (1353)
|++||||+||++||.+|+.||.+||+||.+|+.+|++..++|+++++|.+.. .+. +. +..
T Consensus 288 P~~skl~~Fgv~Al~~frskL~~Yp~yC~~Il~~~~~s~~~~~l~~~I~~~~---~sa----na---~~~---------- 347 (1591)
T KOG1831|consen 288 PPSSKLFIFGVQALLPFRSKLLDYPKYCFDILSIPPFSKFRPHLYDSIWETA---TSA----NA---TTR---------- 347 (1591)
T ss_pred CChhHHHHHHHHHHHHHHHHhcchHHHHHHHHhCcchhhccHHHHHHHHhhh---hhc----cC---CCc----------
Confidence 9999999999999999999999999999999999999999999999997732 111 00 000
Q ss_pred CCCcccCCCcccccchhhhhHHhhhhccccccccccccccccCCCCCCcccCCCCCccCCCCCCcchhhhcccCCCcccc
Q 000683 846 GNGEVSGSGITQLGQQLSSQIQLQQRSESVVDDRHKVSAASSSDMKPLLSSIGQPSSVAPLGDTSSAQKLHNAVSAPAML 925 (1353)
Q Consensus 846 ~~~~~~~~~~~~~~~q~~~~~~~qq~~~~~l~~~~~~s~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~ 925 (1353)
. ..|..+.+ +..
T Consensus 348 ~-------------------------------------------s~pv~~~~--------p~~----------------- 359 (1591)
T KOG1831|consen 348 K-------------------------------------------SDPVRSAS--------PYL----------------- 359 (1591)
T ss_pred c-------------------------------------------cccchhcc--------ccc-----------------
Confidence 0 00000000 000
Q ss_pred ccCCCccCCCCCccccccccccchhhHHHHhhcCCCCCCCCChhhhhhhhhhhhcCCcccHHHHHHHHHHHhhhcchhhh
Q 000683 926 SISSGFARPSRGVTSTKFGSALNIETLVAAAERRETPIEAPASEVQDKISFIINNISALNVEAKAKEFTEILKEQYYPWF 1005 (1353)
Q Consensus 926 ~~~~~~~~~~~~~~~~~~~~a~nidtl~~~~e~~~~~i~~P~e~vqdKI~FiiNNls~~Nl~~K~~El~~~L~~~y~~WF 1005 (1353)
++. -+...++. .-+.|||.|+|||+|++||+|+.|+.+|++|++++|+++||+||
T Consensus 360 ----~~a------------vs~~~~P~---------n~~~~~e~v~dkilF~lNNlsq~N~~qKvdevk~~ltp~y~~Wf 414 (1591)
T KOG1831|consen 360 ----DSA------------VSKHVEPK---------NAEGPPEDVVDKILFPLNNLSQLNFNQKVDEVKEILTPEYYPWF 414 (1591)
T ss_pred ----ccc------------ccccCCcc---------cccCCchhhhhhheeeechHhhhhhHHHHHHHHHHcChhhHHHH
Confidence 000 00011111 12479999999999999999999999999999999999999999
Q ss_pred hHHHHHhhcccCCchhHHHHHHHHHhCChhHHHHHHHHHHHHHHHHhcccccccChHHHHHHHHhHHhhhhhhhhcCccc
Q 000683 1006 AQYMVMKRASIEPNFHDLYLKFLDKVNSKALNREIVQATYENCKVLLGSELIKSSSEERSLLKNLGSWLGKLTIGRNQVL 1085 (1353)
Q Consensus 1006 A~YLV~kRas~EpN~H~LY~~fld~l~~~~L~~~vl~~Ty~~i~~LL~se~~~~~s~eRslLKNLG~WLG~iTLarNkPI 1085 (1353)
|+|+|+||||+|+|||+||.+|++.+++.. | -+||++|||||||||.|||||||||
T Consensus 415 s~YiV~qR~S~E~Nf~~LYskFi~ai~n~~--------t----------------~~dk~~LKNLgsWLG~iTl~rNkPI 470 (1591)
T KOG1831|consen 415 SQYIVTQRVSKEINFHELYSKFISAIKNSV--------T----------------ESDKRLLKNLGSWLGEITLGRNKPI 470 (1591)
T ss_pred HHHHhhhhhhcccchHHHHHHHHHHHhCcc--------c----------------hhHHHHHHHHHHHHHHHHHhcCCch
Confidence 999999999999999999999999999982 2 1799999999999999999999999
Q ss_pred ccCCCChhHHHHHHHhcCceeEEechhhhhccccCCCccccCCCccHHHHHHHHHHHhcCCccchhhHHHHHHHHhhcCC
Q 000683 1086 RAREIDPKSLIIEAYEKGLMIAVIPFTSKILEPCQSSLAYQPPNPWTMAILGLLAEIYSMPNLKMNLKFDIEVLFKNLGV 1165 (1353)
Q Consensus 1086 ~~k~ld~K~LL~eaY~~g~L~~ViPFV~KVLe~~~~S~vFkPPNPW~m~IL~lL~Ely~~~~LKlnLKFEIEvL~K~L~l 1165 (1353)
++.++|||+||+|||.+|++..|+|||||||+.|.+|+||||||||||+||++|+|+|+.||+|+|||||||||||+|++
T Consensus 471 ~~l~l~~kslLlEaY~sg~ll~VvPFVaKIL~~asksrIFkpPnpW~~gIlklL~ELh~e~d~klnLkFEIEVLlkslN~ 550 (1591)
T KOG1831|consen 471 KELDLDFKSLLLEAYGSGRLLPVVPFVAKILEGASKSRIFKPPNPWTMGILKLLAELHQEADLKLNLKFEIEVLLKSLNV 550 (1591)
T ss_pred HHhhhhHHHHHHHHhccCceeecchHHHHHHHhhhhccccCCCCchHHHHHHHHHHhcccccceeeeeeeeeehhccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccccccccccchhhhhcCCCCCCCCccCCCCCCccCCCCccccCCCCCCCCCCccCCCCCCCCCcccccccccccccC
Q 000683 1166 DMKDITPTSLLKDRKREIEGNPDFSNKDVGASQPQLVPEVKPAIVSPLGHVDLPLDVASPPNSGGPTHLLSQYAAPLRLS 1245 (1353)
Q Consensus 1166 d~~di~ps~~L~~r~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~ 1245 (1353)
++++++|+++++|..+.- +.. . .+.++. .+..+++.. |
T Consensus 551 ~l~~le~~~~lnn~~~i~-~~L-------~----~~~~e~-------h~~~~~~~~---------------q-------- 588 (1591)
T KOG1831|consen 551 ILSELEPSETLNNIIRIK-KQL-------V----LMKLET-------HQSLELEDI---------------Q-------- 588 (1591)
T ss_pred hHhhcchhhHHhhHHhHH-HHH-------c----cCChhh-------ccccccCch---------------h--------
Confidence 999999999999954421 100 0 000110 000111100 0
Q ss_pred cCcchhhHHHhhccCCCCCCcccccccccCCCCCCCcccccC-CCCCCCceEEecCcchhcccchhhhhHHHHHHHHhHH
Q 000683 1246 SGTLMEDEKLAALGISDQLPSAQGLFQASQSQSPFSVSQLST-PIPNIGTHVIINQKLTALGLHLHFQRVVPIAMDRAIK 1324 (1353)
Q Consensus 1246 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~s~~~i~~-~i~~l~~~v~in~~l~~~~~~p~lk~iv~~AierAIr 1324 (1353)
++++ .+ +.+|+|++.+. ...+..+++.+.| ||+.|++|+.|++|+|+
T Consensus 589 --------------------~~~~---~~--~~~fa~~~~n~~t~~~~i~~l~~~~-------~P~~Kh~~~~Aleqsv~ 636 (1591)
T KOG1831|consen 589 --------------------QVTL---GN--TIAFAYDARNVSTATEVIKQLDLRP-------HPDIKHRVQEALEQSVV 636 (1591)
T ss_pred --------------------cccc---cC--CccceecccccchhhhhhhhccCCC-------CccHHHHHHHHHHHHHH
Confidence 0000 00 11266666542 2234445555554 89999999999999999
Q ss_pred hhhhhhhhhhhHHHHHHHHHHHhhcccCC
Q 000683 1325 EIVSGIVQRSVSIATQTTKELVLKVCFLS 1353 (1353)
Q Consensus 1325 EII~PVVeRSVtIA~iTT~elV~KDFA~d 1353 (1353)
|||.||||||+.||++||+.||+||||+|
T Consensus 637 eii~~Vv~rs~~IA~ttTe~lirKDFA~e 665 (1591)
T KOG1831|consen 637 EIIEPVVERSSGIASTTTESLIRKDFALE 665 (1591)
T ss_pred HHHHHHHHHhhceeehhHHHHHHHHHhcc
Confidence 99999999999999999999999999987
No 3
>smart00543 MIF4G Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)
Probab=93.22 E-value=0.84 Score=48.98 Aligned_cols=181 Identities=20% Similarity=0.249 Sum_probs=118.6
Q ss_pred hhhhhhhhcCCcccHHHHHHHHHHHhhhc--chhhhhHHHHHhhcccCCchhHHHHHHHHHhCC--hhHHHHHHHHHHHH
Q 000683 972 DKISFIINNISALNVEAKAKEFTEILKEQ--YYPWFAQYMVMKRASIEPNFHDLYLKFLDKVNS--KALNREIVQATYEN 1047 (1353)
Q Consensus 972 dKI~FiiNNls~~Nl~~K~~El~~~L~~~--y~~WFA~YLV~kRas~EpN~H~LY~~fld~l~~--~~L~~~vl~~Ty~~ 1047 (1353)
.+|.-++|-+|.+|++.-++|+.++.... ...-+... +.+++-.+|++-.+|..++..++. +.+-..+++.++..
T Consensus 2 ~~v~~~lnkLs~~n~~~~~~~l~~~~~~~~~~~~~l~~~-i~~~~~~~~~~~~~ya~L~~~l~~~~~~f~~~ll~~~~~~ 80 (200)
T smart00543 2 KKVKGLINKLSPSNFESIIKELLKLNNSDKNLRKYILEL-IFEKAVEEPNFIPAYARLCALLNAKNPDFGSLLLERLQEE 80 (200)
T ss_pred hHHHHHHhhCCHHHHHHHHHHHHHHHccCHHHHHHHHHH-HHHHHHcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46778999999999999999999888543 33344433 456788999999999999999986 46777788888777
Q ss_pred HHHHhcccccccChHHHHHHHHhHHhhhhhhhhcCcccccCCCChhHHHHHHHhcCce------eEEechhhhhccccCC
Q 000683 1048 CKVLLGSELIKSSSEERSLLKNLGSWLGKLTIGRNQVLRAREIDPKSLIIEAYEKGLM------IAVIPFTSKILEPCQS 1121 (1353)
Q Consensus 1048 i~~LL~se~~~~~s~eRslLKNLG~WLG~iTLarNkPI~~k~ld~K~LL~eaY~~g~L------~~ViPFV~KVLe~~~~ 1121 (1353)
....+... ...++...+|+--+||.+..-+=-+.. .+.+++-+--....- ..-|=.+|.+|+.|..
T Consensus 81 f~~~~e~~----~~~~~~~~~~~i~fl~eL~~~~~i~~~----~i~~~l~~ll~~~~~~~~~~~~~~ve~l~~lL~~~G~ 152 (200)
T smart00543 81 FEKGLESE----EESDKQRRLGLVRFLGELYNFQVLTSK----IILELLKELLNDLTKLDPPRSDFSVECLLSLLPTCGK 152 (200)
T ss_pred HHHHHHHH----HHHhhhhHHhHHHHHHHHHHcccCcHH----HHHHHHHHHHhccCCCCCCCcHHHHHHHHHHHHHhhH
Confidence 76654322 334566678888888888765433322 122222222222211 1345567778887766
Q ss_pred CccccCCCccHHH-HHHHHHHHhcCC---ccchhhHHHHHHHHhh
Q 000683 1122 SLAYQPPNPWTMA-ILGLLAEIYSMP---NLKMNLKFDIEVLFKN 1162 (1353)
Q Consensus 1122 S~vFkPPNPW~m~-IL~lL~Ely~~~---~LKlnLKFEIEvL~K~ 1162 (1353)
.--+ +.+|=.|. ++..+....... .+....+|-++-|+.-
T Consensus 153 ~l~~-~~~~~~~~~~l~~l~~~~~~~~~~~~~~r~~~~l~~l~~l 196 (200)
T smart00543 153 DLER-EKSPKLLDEILERLQDYLLKKDKTELSSRLRFMLELLIEL 196 (200)
T ss_pred HHcC-cccHHHHHHHHHHHHHHHhcccccCCChHHHHHHHHHHHH
Confidence 5333 55555544 556665555554 5677778888877653
No 4
>KOG1831 consensus Negative regulator of transcription [Transcription]
Probab=85.93 E-value=91 Score=43.20 Aligned_cols=124 Identities=20% Similarity=0.165 Sum_probs=88.4
Q ss_pred HHhhcccCCchhHHHHHHHHHhCChhHHHHHHHHHHH-HHHHHhcccccccChHHHHHHHHhHHhhhhhhhhcCcccccC
Q 000683 1010 VMKRASIEPNFHDLYLKFLDKVNSKALNREIVQATYE-NCKVLLGSELIKSSSEERSLLKNLGSWLGKLTIGRNQVLRAR 1088 (1353)
Q Consensus 1010 V~kRas~EpN~H~LY~~fld~l~~~~L~~~vl~~Ty~-~i~~LL~se~~~~~s~eRslLKNLG~WLG~iTLarNkPI~~k 1088 (1353)
+.|==..|++=..||+.+... .+.|-+.+...|.+ -+++...+. |-+...=+=.+..|.++-+..-
T Consensus 658 irKDFA~e~~es~l~~Aa~~M--~r~la~~lAmiTcreplk~am~~n-----------l~~~~~~~l~~~~ai~~a~~t~ 724 (1591)
T KOG1831|consen 658 IRKDFALERDESRLRLAASQM--VRELAAGLAMITCREPLKVAMSSN-----------LVLAALSLLSLMAAIARAADTL 724 (1591)
T ss_pred HHHHHhcccchhHHHHHHHHH--HHHHHHHHHHHhhhhHHHHHHHhh-----------HHHHHhhhhHHHHHHHHHHHHH
Confidence 333346788888888877654 23444444444443 222222221 1111111111577778888888
Q ss_pred CCChhHHHHHHHhcCceeEEechhhhhccccCCCccccCCCccHHHHHHHHHHHhcCC
Q 000683 1089 EIDPKSLIIEAYEKGLMIAVIPFTSKILEPCQSSLAYQPPNPWTMAILGLLAEIYSMP 1146 (1353)
Q Consensus 1089 ~ld~K~LL~eaY~~g~L~~ViPFV~KVLe~~~~S~vFkPPNPW~m~IL~lL~Ely~~~ 1146 (1353)
--|.+.+.+.-.++-++...+-++.+-|++..--+||.+.|||.|.++-.+.+.|++.
T Consensus 725 ~~dNv~l~~~~Iek~a~eka~~dI~~~L~q~~~~Rv~~k~~~~~~~fvD~~~~~~~~~ 782 (1591)
T KOG1831|consen 725 QSDNVELVVKFIEKTAIEKATQDIDSRLEQDICGRVFHKENPEVMPFVDLLSAAYSCT 782 (1591)
T ss_pred HhhchhhHhhhhHHHHHHHHHHHHHHHHHHhhHhheecccCCccccchhhhhhhhhcc
Confidence 8888999999999999999999999999999999999999999999999999999975
No 5
>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 3", and is found in nuclear cap-binding proteins, eIF4G, and UPF2. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA. Nonsense-mediated mRNA decay (NMD) in eukaryotes involves UPF1, UPF2 and UPF3 to accelerate the decay rate of two unique classes of transcripts: (1) nonsense mRNAs that arise through errors in gene expression, and (2) naturally occurring transcripts that lack coding errors but have built-in features that target them for accelerated decay (error-free mRNAs). NMD can trigger decay during any round of translation and can target CBC-bound or eIF-4E-bound transcripts []. UPF2 contains MIF4G domains, while UPF3 contains an RNP domain []. ; GO: 0005515 protein binding, 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A 1HU3_A 3RK6_A ....
Probab=84.72 E-value=2.9 Score=44.72 Aligned_cols=109 Identities=18% Similarity=0.241 Sum_probs=79.1
Q ss_pred hhhhhhhhcCCcccHHHHHHHHHHHhhhc---chhhhhHHHHHhhcccCCchhHHHHHHHHHhCCh---hHHHHHHHHHH
Q 000683 972 DKISFIINNISALNVEAKAKEFTEILKEQ---YYPWFAQYMVMKRASIEPNFHDLYLKFLDKVNSK---ALNREIVQATY 1045 (1353)
Q Consensus 972 dKI~FiiNNls~~Nl~~K~~El~~~L~~~---y~~WFA~YLV~kRas~EpN~H~LY~~fld~l~~~---~L~~~vl~~Ty 1045 (1353)
-||.-++|-+|..|++.-++++.+..... ...-++..+ .++|..+|++..+|..++..+... .+-..+++.+.
T Consensus 2 r~v~~~lnklt~~n~~~~~~~l~~~~~~~~~~~~~~i~~~i-~~~a~~~~~~~~~~a~l~~~l~~~~~~~f~~~ll~~~~ 80 (209)
T PF02854_consen 2 RKVRGILNKLTPSNFESIIDELIKLNWSDDPETLKEIVKLI-FEKAVEEPNFSPLYARLCAALNSRFPSEFRSLLLNRCQ 80 (209)
T ss_dssp HHHHHHHHHCSSTTHHHHHHHHHHHHHHSCHHHHHHHHHHH-HHHHHHSGGGHHHHHHHHHHHHHHCHHHHHHHHHHHHH
T ss_pred chHHHHHHHCCHHHHHHHHHHHHHHHhhccHHHHHHHHHHH-hhhhhcCchHHHHHHHHHHHHhccchhhHHHHHHHHHH
Confidence 36778999999999999999999998766 334444333 457899999999999999998743 45566666666
Q ss_pred HHHHHHh-cccccccChHHHHHHHHhHHhhhhhhhhc
Q 000683 1046 ENCKVLL-GSELIKSSSEERSLLKNLGSWLGKLTIGR 1081 (1353)
Q Consensus 1046 ~~i~~LL-~se~~~~~s~eRslLKNLG~WLG~iTLar 1081 (1353)
+.+.... ..+.......++...+|+.-+||.+....
T Consensus 81 ~~f~~~~~~~~~~~~~~~~~~~~~~~~~fl~eL~~~~ 117 (209)
T PF02854_consen 81 EEFEERYSNEELEENRQSSKQRRRGNIRFLAELFNFG 117 (209)
T ss_dssp HHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHhhhhhhHHHHHHHHHHHHhhhhhHHHhhHhhc
Confidence 5555411 01222345667888899999999988654
No 6
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=58.77 E-value=78 Score=31.22 Aligned_cols=71 Identities=15% Similarity=0.322 Sum_probs=56.0
Q ss_pred CHHHHHHHHHHhhcCCcccchhhHHHHHHhHHhhhccCCCCcHHHHHHHHHHHHHHhhhhccchhhHHHHHHHHHHHhcC
Q 000683 686 TIEAMVQMLARFKESSVKREHSIFECMIGNLFEEYRFFPKYPERQLRIAAVLFGSIIKHQLVTHLTLGIALRGVLDALRK 765 (1353)
Q Consensus 686 sI~~ii~~L~~~k~S~~~reqdvFaCMIh~LFdEYrff~~YP~~eL~iTA~LFG~lI~~~Lv~~~~L~iALr~ILeAlr~ 765 (1353)
..+|.+..+++++-+ ....++..-+|+..+|+ =..+-..++.|+..+++.++++...+.-|+.-+++.+..
T Consensus 17 d~~ea~~~l~el~~~--~~~~~vv~~~l~~~le~-------~~~~r~~~~~Ll~~L~~~~~~~~~~~~~gf~~~l~~l~D 87 (113)
T PF02847_consen 17 DVDEAVECLKELKLP--SQHHEVVKVILECALEE-------KKSYREYYSKLLSHLCKRKLISKEQFQEGFEDLLESLED 87 (113)
T ss_dssp -HHHHHHHHHHTT-G--GGHHHHHHHHHHHHHTS-------SHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHhCCC--ccHHHHHHHHHHHHhhc-------cHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhHhhh
Confidence 678888888888666 56678888888888888 456667799999999999999998888888888777644
No 7
>COG5088 SOH1 Rad5p-binding protein [General function prediction only]
Probab=58.13 E-value=23 Score=35.06 Aligned_cols=89 Identities=21% Similarity=0.293 Sum_probs=65.7
Q ss_pred ccHHHHHHHHHHHhhhcchhhhhHHHHHhhcccCCchhHHHHHHHHHhCChhHHHHHHHHHHHHHHHHhcccccccChHH
Q 000683 984 LNVEAKAKEFTEILKEQYYPWFAQYMVMKRASIEPNFHDLYLKFLDKVNSKALNREIVQATYENCKVLLGSELIKSSSEE 1063 (1353)
Q Consensus 984 ~Nl~~K~~El~~~L~~~y~~WFA~YLV~kRas~EpN~H~LY~~fld~l~~~~L~~~vl~~Ty~~i~~LL~se~~~~~s~e 1063 (1353)
+-+|-..+=+.-+-.+.|..|+++.=.-+ -..-.-|++.++--.+|+.-+.|+--+.--|-.||++....+.-+|
T Consensus 15 sRFE~ELEFvQ~L~Np~Yl~~Ltq~~~fe-----se~F~~YL~YlEYWr~PeYs~fivYP~CL~iL~lLn~~~~~~~vs~ 89 (114)
T COG5088 15 SRFEVELEFVQSLANPQYLTLLTQQQIFE-----SENFKNYLKYLEYWRNPEYSQFIVYPNCLFILKLLNGFMESAIVSE 89 (114)
T ss_pred chhHHHHHHHHHhcCHHHHHHHHHhhhhc-----CHHHHHHHHHHHHhhCCcccceeechhHHHHHHHhcchhHhhhhhh
Confidence 34444443333333578888887765443 2344569999999999999999988887778888998888778889
Q ss_pred HHHHHHhH-----Hhhhhh
Q 000683 1064 RSLLKNLG-----SWLGKL 1077 (1353)
Q Consensus 1064 RslLKNLG-----~WLG~i 1077 (1353)
-.++|.|| -|||+.
T Consensus 90 ~~l~~~l~e~qy~~Wlnk~ 108 (114)
T COG5088 90 DGLLEGLDELQYPQWLNKM 108 (114)
T ss_pred hHHHHhhhHHHHHHHHHHH
Confidence 99999998 488765
No 8
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=40.03 E-value=90 Score=29.55 Aligned_cols=60 Identities=17% Similarity=0.225 Sum_probs=44.2
Q ss_pred cHHHHHHHHHhhhhhchHHHHHHHHHHHhhccchhhHHHHhhhhhcccCCCCCCChhhHHHHH
Q 000683 8 VPSQIRFLLQSLNEANADSVFRELCQFIEYGIEGSTMMLQTCMDHLNLHGTGLKNPQLESVVA 70 (1353)
Q Consensus 8 ~~~qI~~Lv~~l~kkn~~~~~~el~qlv~~G~ea~~~lLr~~l~~~~~~~~~~k~~~~~~LL~ 70 (1353)
...+|+.+++.+-+++|+..+..+.+++.-|+.+. .+++.+.+.+--. +..+..|.+++.
T Consensus 4 ~~~~i~~i~~~~~~~~~~~~~~~~~~l~~~G~s~~-~Il~~l~~~l~~~--~~~~~~k~~i~~ 63 (89)
T PF08542_consen 4 PPEVIEEILESCLNGDFKEARKKLYELLVEGYSAS-DILKQLHEVLVES--DIPDSQKAEILK 63 (89)
T ss_dssp -HHHHHHHHHHHHHTCHHHHHHHHHHHHHTT--HH-HHHHHHHHHHHTS--TSSHHHHHHHHH
T ss_pred CHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCCHH-HHHHHHHHHHHHh--hccHHHHHHHHH
Confidence 46789999999999999999999999986699988 5666777765332 445666665543
No 9
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=34.71 E-value=2e+02 Score=28.35 Aligned_cols=71 Identities=13% Similarity=0.302 Sum_probs=60.0
Q ss_pred CHHHHHHHHHHhhcCCcccchhhHHHHHHhHHhhhccCCCCcHHHHHHHHHHHHHHhhhhccchhhHHHHHHHHHHHhcC
Q 000683 686 TIEAMVQMLARFKESSVKREHSIFECMIGNLFEEYRFFPKYPERQLRIAAVLFGSIIKHQLVTHLTLGIALRGVLDALRK 765 (1353)
Q Consensus 686 sI~~ii~~L~~~k~S~~~reqdvFaCMIh~LFdEYrff~~YP~~eL~iTA~LFG~lI~~~Lv~~~~L~iALr~ILeAlr~ 765 (1353)
..+|.+..+++++.+ ....++....|+--+|| + +++-..++.|+..+.+.++++...+.-|+.-+++.+.+
T Consensus 17 D~~ea~~~l~~L~~~--~~~~~vv~~~i~~~le~-~------~~~~~~~~~Ll~~L~~~~~~~~~~~~~~f~~~~~~l~d 87 (113)
T smart00544 17 DTDEAVHCLLELKLP--EQHHEVVKVLLTCALEE-K------RTYREMYSVLLSRLCQANVISTKQFEKGFWRLLEDIED 87 (113)
T ss_pred CHHHHHHHHHHhCCC--cchHHHHHHHHHHHHcC-C------ccHHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhhChh
Confidence 678888888888766 47888999999998998 2 45667799999999999999999999999998888866
No 10
>KOG3769 consensus Ribonuclease III domain proteins [Translation, ribosomal structure and biogenesis]
Probab=33.54 E-value=92 Score=36.76 Aligned_cols=50 Identities=18% Similarity=0.126 Sum_probs=44.2
Q ss_pred hccCCChHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHhhccch
Q 000683 121 LSDSENLDALMCGKNFCMAQIERLCANPVPMNSAEQIQNIIMFLQRSSDL 170 (1353)
Q Consensus 121 L~~S~n~e~r~~a~~f~~~~i~el~~n~~~~~s~e~lh~il~~l~~~~gl 170 (1353)
+-.-+|.|+...|++|+...+.+.+..--..+|+|+||.|+.++...+-|
T Consensus 111 ~~~~~N~~L~~~Gk~~~~~~v~~~l~~kyPrlP~E~l~ai~n~ll~ee~L 160 (333)
T KOG3769|consen 111 NPQYSNEELVEIGKQFLSFYVTEYLKCKYPRLPEEGLHAIVNGLLGEEVL 160 (333)
T ss_pred cCCcchHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHHHHHhhhHHHH
Confidence 45568999999999999999999998888999999999999998775544
No 11
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=26.26 E-value=1.4e+02 Score=37.67 Aligned_cols=172 Identities=20% Similarity=0.310 Sum_probs=100.9
Q ss_pred hhhhhhhhhhhhcCCcccHHHHHHHHHHHhhhcchh---hhhHHHHHhhcccCCchhHHHHHHHHHhCCh--hHHHHHHH
Q 000683 968 SEVQDKISFIINNISALNVEAKAKEFTEILKEQYYP---WFAQYMVMKRASIEPNFHDLYLKFLDKVNSK--ALNREIVQ 1042 (1353)
Q Consensus 968 e~vqdKI~FiiNNls~~Nl~~K~~El~~~L~~~y~~---WFA~YLV~kRas~EpN~H~LY~~fld~l~~~--~L~~~vl~ 1042 (1353)
|.+..+|.=+|||+..+|+..-+. ++++++.-. -|.. =||+=.+--|+|-.+|..++--||++ .+=..+++
T Consensus 162 EalkksInglInkvn~sNi~~ii~---eLfqeNiirgRgl~cr-sv~~aq~asp~ft~vyaALvAviNskfP~IgElLlk 237 (739)
T KOG2140|consen 162 EALKKSINGLINKVNASNIQEIIR---ELFQENIIRGRGLLCR-SVMQAQAASPGFTPVYAALVAVINSKFPQIGELLLK 237 (739)
T ss_pred HHHHHHhHHHHhhhhHHHHHHHHH---HHHHHHHHhccchhHH-HHHHHHhcCCCCcHHHHHHHHHHccCCchHHHHHHH
Confidence 567889999999999999865554 444444321 1111 25555567799999999999999987 33344444
Q ss_pred HHHHHHHHHhcccccccChHHHHHHHHhHHhhhhhhhhcCcccccCCCChh--HHHHHHHhcCceeEEechh----hhhc
Q 000683 1043 ATYENCKVLLGSELIKSSSEERSLLKNLGSWLGKLTIGRNQVLRAREIDPK--SLIIEAYEKGLMIAVIPFT----SKIL 1116 (1353)
Q Consensus 1043 ~Ty~~i~~LL~se~~~~~s~eRslLKNLG~WLG~iTLarNkPI~~k~ld~K--~LL~eaY~~g~L~~ViPFV----~KVL 1116 (1353)
....+.+.=.+ -.|+...-|--.++.-+ -|+-+-|.-+.+. -||+|-=..+.+.++|-|+ +|..
T Consensus 238 rLilqf~r~f~-------RnDk~~c~~~~kfiahL---inq~VahEIv~Leil~lLLe~PTddSvevaI~flkecGakL~ 307 (739)
T KOG2140|consen 238 RLILQFKRSFR-------RNDKVSCLNASKFIAHL---INQQVAHEIVALEILTLLLERPTDDSVEVAIAFLKECGAKLA 307 (739)
T ss_pred HHHHHHHHHhc-------ccchHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHH
Confidence 44433333222 12333333333332222 2333444433333 2344433335566666665 2333
Q ss_pred cccCCCccccCCCccHHHHHHHHHHHhcCCccchhhHHHHHHHHhh
Q 000683 1117 EPCQSSLAYQPPNPWTMAILGLLAEIYSMPNLKMNLKFDIEVLFKN 1162 (1353)
Q Consensus 1117 e~~~~S~vFkPPNPW~m~IL~lL~Ely~~~~LKlnLKFEIEvL~K~ 1162 (1353)
+=.... ..+|..=|.=|-|..+|--.+.|=||+||.-
T Consensus 308 ~VSpr~---------~n~IfErlR~ILhe~Eld~rvqy~iEtlf~i 344 (739)
T KOG2140|consen 308 EVSPRA---------LNGIFERLRYILHEGELDRRVQYMIETLFQI 344 (739)
T ss_pred HhChHH---------HhHHHHHHHHHHhHhhHHHHHHHHHHHHHHH
Confidence 322221 4567777888888889999999999999964
No 12
>PF08514 STAG: STAG domain ; InterPro: IPR013721 STAG domain proteins are subunits of cohesin complex - a protein complex required for sister chromatid cohesion in eukaryotes. The STAG domain is present in Schizosaccharomyces pombe (Fission yeast) mitotic cohesin Psc3, and the meiosis specific cohesin Rec11. Many organisms express a meiosis-specific STAG protein, for example, mice and humans have a meiosis specific variant called STAG3, although budding yeast does not have a meiosis specific version [].
Probab=22.21 E-value=41 Score=34.41 Aligned_cols=61 Identities=23% Similarity=0.434 Sum_probs=40.5
Q ss_pred HHHHHhhcccCCchhHHHHHHHHHhCChhHHHHHHHHHHHHHHHHhcccccccChHHHHHHHHhHHhhhhhhhhcCcccc
Q 000683 1007 QYMVMKRASIEPNFHDLYLKFLDKVNSKALNREIVQATYENCKVLLGSELIKSSSEERSLLKNLGSWLGKLTIGRNQVLR 1086 (1353)
Q Consensus 1007 ~YLV~kRas~EpN~H~LY~~fld~l~~~~L~~~vl~~Ty~~i~~LL~se~~~~~s~eRslLKNLG~WLG~iTLarNkPI~ 1086 (1353)
.|-...|.+.=.+|+..|.+|++.| +...+. -+|- |-.++.++-.||..++-+.-||++
T Consensus 5 ~YPli~k~~~~k~Fr~~~~~F~~~l---------v~~~~~---~~Ly---------d~~l~~~l~~wl~~lS~S~~R~fR 63 (118)
T PF08514_consen 5 DYPLISKGKKFKKFRKNFCEFFDQL---------VEQCHS---SILY---------DDYLMDNLISWLTALSSSKVRPFR 63 (118)
T ss_pred cCCCcCCCcccHHHHHHHHHHHHHH---------HHHhcc---cccc---------cHHHHHHHHHHHHHhccCCceeeh
Confidence 3555555555566777777777552 222221 1111 118999999999999999999999
Q ss_pred cC
Q 000683 1087 AR 1088 (1353)
Q Consensus 1087 ~k 1088 (1353)
|.
T Consensus 64 hT 65 (118)
T PF08514_consen 64 HT 65 (118)
T ss_pred HH
Confidence 84
No 13
>PF01603 B56: Protein phosphatase 2A regulatory B subunit (B56 family); InterPro: IPR002554 Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism. The ability of this widely distributed heterotrimeric enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits, this family is called the B56 family [].; GO: 0008601 protein phosphatase type 2A regulator activity, 0007165 signal transduction, 0000159 protein phosphatase type 2A complex; PDB: 2NYM_B 2NYL_B 2IAE_E 2NPP_B 3FGA_B 2JAK_A.
Probab=21.35 E-value=1.1e+03 Score=29.09 Aligned_cols=109 Identities=10% Similarity=0.185 Sum_probs=55.7
Q ss_pred ccchHHHHHHHHHhhc--CCCCchHHHHHHHHH-HHHhhccCCCccCCCCCCCCCCCCCchhHH--HHHHHHHHHhhcc-
Q 000683 610 YMEKIPVILKLLKAHI--GLITSTKLSEEIEKF-QAVVLDSTPRLQNGEAADSSTSEGYADDIE--AEANSYFHQMFSG- 683 (1353)
Q Consensus 610 ~~et~~~ll~~L~~~~--~~~~s~~~~e~l~~~-~~~~~~~~prL~n~~~~d~~~~~~~~~dVE--~Ean~yfqkmY~~- 683 (1353)
.-+|+.-+++.+.+.. +. .+++....+.+| ..++.+..|...+.....+....-..+.-+ .-+-+.|.++...
T Consensus 43 K~~~L~el~~~v~~~~~~~~-l~e~~~~~i~~Mi~~NifR~lP~~~~~~~~~~~d~~~~e~~WpHL~~vY~il~~~i~~~ 121 (409)
T PF01603_consen 43 KRQTLNELVDYVSNSRIQGI-LTEPVYPEIFNMISANIFRPLPPIPNPSFDPDDDEPFLEPSWPHLQLVYEILLRFIESP 121 (409)
T ss_dssp HHHHHHHHHHHHCSSS--SS-S-TTSHHHHHHHHHHHH-S-----SS--S-GGG------TTHHHHHHHHHHHHHHHTST
T ss_pred HHHHHHHHHHHHhCcccccc-CCHHHHHHHHHHHHHhccCCCCCcccccCCccccccccccccHhHHHHHHHHHHHHHCc
Confidence 3456777777776654 33 355666665554 446666667665432110000000001111 1344455555542
Q ss_pred cc-----CH-HHHHHHHHHhhcCCcccchhhHHHHHHhHHhh
Q 000683 684 QL-----TI-EAMVQMLARFKESSVKREHSIFECMIGNLFEE 719 (1353)
Q Consensus 684 ei-----sI-~~ii~~L~~~k~S~~~reqdvFaCMIh~LFdE 719 (1353)
.. -+ ..+|..|-..=+|+|+||||....++|.+|+.
T Consensus 122 ~~~~~~~~i~~~fi~~Ll~l~~S~D~rER~~lk~~l~~iy~k 163 (409)
T PF01603_consen 122 PFDPAKKYIDQKFIKKLLELFDSPDPRERDYLKTILHRIYGK 163 (409)
T ss_dssp T--CCTTTS-HHHHHHHHHTTTSSTHHHHHHHHHHHHHHHHH
T ss_pred cccHHHHHcCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Confidence 11 12 36777777777889999999999999999886
No 14
>PF12054 DUF3535: Domain of unknown function (DUF3535); InterPro: IPR022707 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 439 to 459 amino acids in length. This domain is found associated with PF00271 from PFAM, PF02985 from PFAM, and PF00176 from PFAM. This domain has two completely conserved residues (P and K) that may be functionally important.
Probab=20.39 E-value=3.8e+02 Score=33.56 Aligned_cols=109 Identities=12% Similarity=0.218 Sum_probs=64.5
Q ss_pred CCCCCCCc-hhHHHHHHHHHHHhhccc-----cCHHHHHHHHHHhhcCCcccchhhHHHHHHhHHhhhccCCCCcHHHHH
Q 000683 659 SSTSEGYA-DDIEAEANSYFHQMFSGQ-----LTIEAMVQMLARFKESSVKREHSIFECMIGNLFEEYRFFPKYPERQLR 732 (1353)
Q Consensus 659 ~~~~~~~~-~dVE~Ean~yfqkmY~~e-----isI~~ii~~L~~~k~S~~~reqdvFaCMIh~LFdEYrff~~YP~~eL~ 732 (1353)
...+..|+ +++++-++.+|.+++..- ++.-+.++--+ +.+.+. .++|+.- +=....+
T Consensus 229 ~~~p~~fsi~~A~~v~~~~~~~l~~~l~~~~k~~a~~~Le~~r----------~~l~~a-----i~~~~~~--~~~~~~~ 291 (441)
T PF12054_consen 229 EAGPEAFSIEQAEKVVGEDFEKLKKSLSPSQKLSALQALEDRR----------QRLQAA-----IEEAKEV--QTSRDVR 291 (441)
T ss_pred ccCCccCCHHHHHHHHHHHHHHHHHhcCCcccchHHHHHHHHH----------HHHHHH-----HHHHHHH--HHHHHHH
Confidence 34556777 788999999999998832 21122222111 111111 1222210 1112233
Q ss_pred HHHHHHHHHhhhhccchhhHHHHHHHHHHHhcCCCCCccccHHHHHHHHHHHh
Q 000683 733 IAAVLFGSIIKHQLVTHLTLGIALRGVLDALRKPADSKMFVFGTKALEQFVDR 785 (1353)
Q Consensus 733 iTA~LFG~lI~~~Lv~~~~L~iALr~ILeAlr~p~~skmf~FGi~AL~qF~~R 785 (1353)
+.|.+=|.+|..+-++.. |.=-+|-+.|++|+..+..+-+-+-.||-.|...
T Consensus 292 V~Aa~A~A~v~l~~lP~K-LnPiIrpLMdSIK~Een~~LQ~rsA~slA~Li~~ 343 (441)
T PF12054_consen 292 VLAAAASALVALGGLPKK-LNPIIRPLMDSIKREENELLQQRSAESLARLIQL 343 (441)
T ss_pred HHHHHHHHHHHhccCCCC-ccHHHHHHHHHhhccccHHHHHHHHHHHHHHHHH
Confidence 345556677776666543 6777899999999988887777888888777655
No 15
>PRK00218 putative lysogenization regulator; Reviewed
Probab=20.05 E-value=2.5e+02 Score=31.82 Aligned_cols=90 Identities=20% Similarity=0.363 Sum_probs=60.2
Q ss_pred chhhHHHHHHhHHhhhccCCCCcHHHHHHHHHHHHHHhhhhccchhhHHHHHHHHHHHhcC---CCCCc--cccHHHHHH
Q 000683 705 EHSIFECMIGNLFEEYRFFPKYPERQLRIAAVLFGSIIKHQLVTHLTLGIALRGVLDALRK---PADSK--MFVFGTKAL 779 (1353)
Q Consensus 705 eqdvFaCMIh~LFdEYrff~~YP~~eL~iTA~LFG~lI~~~Lv~~~~L~iALr~ILeAlr~---p~~sk--mf~FGi~AL 779 (1353)
|.+-|.|+|++||.- +| ..|..+||+ +. .|..+|+.+.+.|.. +.+.. -|-+|+.+|
T Consensus 32 d~~~~~~~l~Sll~~------~p----~st~~VyG~-~~-------~L~~Gl~~L~~~L~~~~~~~~~el~RY~~~ll~L 93 (207)
T PRK00218 32 DEDALETSLNSLLVT------NP----SSTLDVYGG-EA-------NLRLGLETLLNQLNSSRQGLDAELTRYALSLLAL 93 (207)
T ss_pred CHHHHHHHHHHHHhc------CC----CCHHHHhCC-cH-------HHHHHHHHHHHHHccCCCCcchHHHHHHHHHHHH
Confidence 567899999999976 45 457788998 32 278888999888873 33333 466777777
Q ss_pred HHHHHhhhhhhHHHHHHhc--------ccccccccHHHHHHHHH
Q 000683 780 EQFVDRLIEWPQYCNHILQ--------ISHLRSTHAELVAFIER 815 (1353)
Q Consensus 780 ~qF~~RL~ewPqyC~~Ll~--------ip~L~~~~p~l~~~ie~ 815 (1353)
|+ ||.-=|..-..|.+ ..||...|+.++..+-.
T Consensus 94 Er---kL~k~~~~~~~L~~ri~~~~rQ~~hf~~~~~~via~lA~ 134 (207)
T PRK00218 94 ER---KLSKNPDALNTLGERINQIQRQLEHFDLLHENVIANLAG 134 (207)
T ss_pred HH---HHccCHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 76 55556666555543 35665567777765433
Done!