Query 000087
Match_columns 2284
No_of_seqs 216 out of 285
Neff 5.9
Searched_HMMs 46136
Date Thu Mar 28 17:30:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000087.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000087hhsearch_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 2E-293 4E-298 2664.5 95.3 1727 168-2271 231-1991(2005)
2 KOG1831 Negative regulator of 100.0 3E-291 7E-296 2711.4 93.2 1470 395-2272 82-1578(1591)
3 PF04054 Not1: CCR4-Not comple 100.0 2E-115 5E-120 1066.2 30.8 366 1888-2263 1-379 (379)
4 PF12842 DUF3819: Domain of un 100.0 2.5E-46 5.5E-51 405.0 17.8 145 1171-1315 1-147 (147)
5 KOG1831 Negative regulator of 97.5 0.11 2.3E-06 72.0 34.3 294 873-1299 658-952 (1591)
6 smart00543 MIF4G Middle domain 91.5 1.5 3.2E-05 50.4 11.7 181 835-1025 2-196 (200)
7 KOG1467 Translation initiation 83.8 3.3 7.1E-05 53.2 8.4 127 1181-1314 241-387 (556)
8 PF02854 MIF4G: MIF4G domain; 79.2 5.6 0.00012 45.7 7.9 108 836-944 3-117 (209)
9 PF02847 MA3: MA3 domain; Int 42.3 1.7E+02 0.0037 30.8 9.9 71 549-628 17-87 (113)
10 COG5088 SOH1 Rad5p-binding pro 36.9 73 0.0016 33.4 5.6 89 847-940 15-108 (114)
11 cd00686 Terpene_cyclase_cis_tr 28.1 95 0.0021 39.5 5.8 73 1939-2030 113-199 (357)
12 smart00544 MA3 Domain in DAP-5 24.4 3.6E+02 0.0078 28.5 8.7 71 549-628 17-87 (113)
13 PRK00218 putative lysogenizati 20.5 2.1E+02 0.0046 34.2 6.4 90 568-678 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=1.7e-293 Score=2664.48 Aligned_cols=1727 Identities=28% Similarity=0.426 Sum_probs=1405.3
Q ss_pred CCCCCCCHHHHHHHHHhhCCCCCHHHHHHhcCCCCCCCCChhhHHHHHHHHhh-hcCCCcccccccCCcccChhh-hHHH
Q 000087 168 PPLSSWNVDVLVKAIKQLAPNTNWIRVVENLDYEGFYIPTEEAFSFFMSVYKY-ACQEPFPLHAVCGSVWKNTEG-QLSF 245 (2284)
Q Consensus 168 ~~~~~Wn~~v~v~alk~~~p~lnW~~Vi~~lD~~~f~i~d~~~l~ll~~~~~~-~~~~~fpi~~l~~~~W~N~~~-Qlsf 245 (2284)
++.+.||.-..+.+++..+..+||.+|..+||.+.|.|+....+..++++|-. +.+.+||.+.+|. .|||... ||++
T Consensus 231 ~D~~~w~~v~~~~a~~s~~e~iNW~~v~s~f~~~~F~i~~l~p~~v~~~c~f~~~~~~~v~~eff~~-~Wkn~~~~~l~i 309 (2005)
T COG5103 231 PDRGEWNLVAIVGAMKSNLEEINWRDVYSCFLDVNFSIWTLEPLYVIIDCWFYISGIITVPYEFFFK-RWKNERAQILFI 309 (2005)
T ss_pred ccccccchHHHHHHHHhhhhhcCHHHHHHHhcCcceeeccCcchHHHHHHHHHHhcCCCccHHHHHH-HhcchhhhhHhh
Confidence 34678999999999999999999999999999999999977766666666555 4567899999995 9999999 5666
Q ss_pred HHHHhhCCCCccccCC-CCcccccccCCCCccccc-cccccccchHHHHHHHHHhhhcCchHHHHHHhhhhhhcChhHHH
Q 000087 246 LRYAVASPPEVFTFAH-SARQLPYVDAVPGLKLQS-GQANHAWLCLDLLDVLCQLSEMGHASFARSMLEYPLKQCPEMLL 323 (2284)
Q Consensus 246 l~~~l~~p~~~f~f~~-~~~~~v~~d~~~~~~~~~-~~~~~~W~sldl~e~L~~Lae~~~~~~v~~l~~~p~~~~pe~ll 323 (2284)
.-|..+.+...|+... .+.+.|..+...+.+... -...+++||.+|++++. +++.....-..++| +...||.+.
T Consensus 310 ~lhi~s~~~~~fd~~Nv~~tr~Vs~~~~~~~~~~ny~~~~snlNc~el~Q~~~-l~~~p~i~y~~~lF---lN~~pE~~~ 385 (2005)
T COG5103 310 RLHIESDEKRTFDYSNVFFTRIVSIEDSRGHRFKNYMGYESNLNCVELFQCIM-LGSLPLIEYIARLF---LNKSPEWCA 385 (2005)
T ss_pred heeeeecccchheecccceeEEEeeecCchHHHHHHHHHhcccCHHHHHHHHH-hccchHHHHHHHHH---hccCHHHHH
Confidence 6677777777887754 345555554443333222 24779999999999993 33332222223466 789999999
Q ss_pred HHhhcc-----CcchhHHHHHHHHhhhHHhhc-CCCchHHHHHHHhhCChhHHHHHHHhhccCCccHHHHHHHHHHhhhh
Q 000087 324 LGMAHI-----NTAYNLIQYEVSFAVFPMIIK-STMSNGMILHIWHVNPNIVLRGFVDAQNMEPDCTIRILEICQELKIL 397 (2284)
Q Consensus 324 lgl~~i-----~~~~~~l~~ell~~l~~~fl~-~~~~~~vi~~lW~~~~~~~~~~l~d~y~~d~~~l~rIldvaqelk~L 397 (2284)
.||..+ +-.||+.+.+.+...+-+++. ..++++|+..+.+.+|+++++...-...+|...++|++|+.-|+|.|
T Consensus 386 a~L~~~~~~f~~L~~N~v~~s~if~~ll~~f~n~~p~sFvfv~~~rT~p~~~~~~~r~v~~kd~~pv~~~l~~~le~~~l 465 (2005)
T COG5103 386 AGLGFVQPKFSPLAWNPVQESRIFEELLMGFANGAPNSFVFVVLFRTHPEMMLQKSRLVLAKDGIPVSRLLDIFLEHKML 465 (2005)
T ss_pred HHHHHhhhhhhhhhcCchHHHHHHHHHHHHHhcCCCCceEEEEEEecCHHHHHHHHHHHHhcCCCcHHHHHHHHHhcCch
Confidence 999754 447999999988888888775 55889999999999999999999877899999999999999999999
Q ss_pred hhhhcccCchhHHHHHHHhhcccccCHHHHHHHHhhcCcc-h----HHHHHHHHHHHHhhcccccccCCCCCCCcccccc
Q 000087 398 SSVLEMIPSPFAIRLAVIASQKELVDLEKWLSINLSTYKD-V----FFEECLKFVKEVQFGRSQDFSAQPFHHSGALLNL 472 (2284)
Q Consensus 398 ~~lL~~~p~~f~idLA~lAsrre~l~lekWl~~~l~~~~~-~----f~~a~l~FL~~k~~~~~~~~~~~~~~~~~~~~~L 472 (2284)
+.+.|..|..|++|+++|++.|+.++|..|+..++....+ + |+...++||+.|+.......+.+ ..+-+ +
T Consensus 466 ~~V~n~lP~~f~~~i~vL~~aR~~l~~~~Wl~~~~~~~~dad~~NVfvv~~~~~l~sk~s~~k~p~~q~---ee~~~--f 540 (2005)
T COG5103 466 PLVSNLLPPEFCFDIIVLSSARDHLNLGIWLSNNLTTRKDADGLNVFVVSLVQYLDSKVSKHKEPEKQK---EESVM--F 540 (2005)
T ss_pred hhhhhcCCHHHHHHHHHHHHHHHhcchhhhcccCceeeecCCcccchHHHHHHHHHHHHhhcCChhhhc---cccee--e
Confidence 9999999999999999999999999999999999987665 3 99999999999997543311111 11223 3
Q ss_pred cchhHHHHHHHHHhhhCCCCchHHHHHHHHHHHHhhccCCCCCCCC-CCCCC-----CCCCCchhHHHHHHHHHHHhhcc
Q 000087 473 YMEKIPVILKLLKAHIGLITSTKLSEEIEKFQAVVLDSTPRLQNGE-AADSS-----TSEGYADDIEAEANSYFHQMFSG 546 (2284)
Q Consensus 473 ~~etv~~lL~~L~~~~~~~~s~~l~e~l~~~~~~~i~~~PrL~n~~-~~d~~-----~~~~~~~dIE~Ean~yfqkmYs~ 546 (2284)
+..|+-.+|..+...... -.+.++.++..|++.||||++.| +||+. +.++++.|||+||.+|||+||++
T Consensus 541 ~~~tvieil~t~~~~V~q-----~~~~~k~~~~~~l~~fprli~~G~~~Ds~v~at~tt~s~~~dIE~E~~sy~q~~y~~ 615 (2005)
T COG5103 541 PLNTVIEILGTFTKAVEQ-----YIRILKPETVVVLNEFPRLIPHGLRRDSIVAATNTTRSKEIDIEEEASSYIQQIYNS 615 (2005)
T ss_pred ehhhHHHHHHHhHHHHHH-----HHHhcCcceEehHhhhhhhccCCCCcchhhhccCcccccCccHHHHHHHHHHHHHHh
Confidence 445655555544332211 15677888889999999999999 88873 45679999999999999999999
Q ss_pred CCCHHHHHHHHHHhhcCCcccchhhHHhHHHhhhhhhccCCCCcHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHHh
Q 000087 547 QLTIEAMVQMLARFKESSVKREHSIFECMIGNLFEEYRFFPKYPERQLRIAAVLFGSIIKHQLVTHLTLGIALRGVLDAL 626 (2284)
Q Consensus 547 eisI~~iv~~L~r~K~S~~~rdqdiFaCMIh~LFdEYrFf~~YP~~eL~iTAvLFG~lI~~~Lv~~~~L~iALr~ILeAl 626 (2284)
+++|+++|+.||+|++|++|||+|+|+|+-|.|||||+||++||+++|++|||||||||+++|+++.+|++|+|||..++
T Consensus 616 ~~~I~~~I~~l~~f~~senprd~elfsci~hal~~ey~ff~dyPl~ALaltavLfGslI~f~ll~~~~L~vA~ryI~~~l 695 (2005)
T COG5103 616 QRGIESSINQLKEFLRSENPRDKELFSCIFHALLEEYGFFYDYPLSALALTAVLFGSLIKFRLLPKPYLRVAIRYIKGSL 695 (2005)
T ss_pred cccHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHhcccccCcchHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCcccchHHHHHHHHHHhhhhhhHHHHHHhcccccccccHHHHHHHHHHHHhhccCCCCCCCCCCCcccccccccc
Q 000087 627 RKPADSKMFVFGTKALEQFVDRLIEWPQYCNHILQISHLRSTHAELVAFIERALARISSGHLESDGASNPAAHQHVSSQA 706 (2284)
Q Consensus 627 rkp~~SkMf~FGiqAL~qF~~RL~EwPqyC~~Ll~ip~L~~~~p~l~~~ie~~l~~~~~~~~~~~~~~~~~~~q~~~~q~ 706 (2284)
++|++||||+||+|||++|+.||++||+||+.++.||.|+. .+++|+.|-++.. ..+. .
T Consensus 696 k~P~~skmf~Fg~qal~~Fq~kLp~Yp~yc~~vl~ip~l~~-r~~iy~sivem~s----~eNt-------~--------- 754 (2005)
T COG5103 696 KHPENSKMFSFGFQALEVFQEKLPSYPSYCSEVLEIPTLNN-RILIYKSIVEMDS----NENT-------E--------- 754 (2005)
T ss_pred cCCCchhhHHHHHHHHHHHHHhhhhhhHHHHHHhccccccc-chHHHHHHHHHHh----ccCC-------c---------
Confidence 99999999999999999999999999999999999999965 9999998876642 1100 0
Q ss_pred cCCCCCccCCcccccccchhhHHHhhhcccccccccccccccccCCCCCCcccCCCCCCcCCCCCCchhhhhcccCCCcc
Q 000087 707 TSGNGEVSGSGITQLGQQLSSQIQLQQRSESVVDDRHKVSAASSSDMKPLLSSIGQPSSVAPLGDTSSAQKLHNAVSAPA 786 (2284)
Q Consensus 707 ~~~~~~~~~~~~~~~~~~~~~~~~~qq~~~~~l~~~~~~~~~~~~~~~p~~~s~~~~~~~~~~~~~~~~~~~~~~p~~~~ 786 (2284)
.+.++|.-+.++. .
T Consensus 755 -------------------------------------------~Eka~p~~pm~pl-------~---------------- 768 (2005)
T COG5103 755 -------------------------------------------VEKANPTHPMLPL-------E---------------- 768 (2005)
T ss_pred -------------------------------------------ccccCCCCcccch-------h----------------
Confidence 0000111000000 0
Q ss_pred ccccCCCccCCCCCccccccccccchHHHHHHhhhcCCCCCCCChhhhHhHhhhhhcCCcccHHHHHHHHHHHhhhcchh
Q 000087 787 MLSISSGFARPSRGVTSTKFGSALNIETLVAAAERRETPIEAPASEVQDKISFIINNISALNVEAKAKEFTEILKEQYYP 866 (2284)
Q Consensus 787 ~~~~~~~~~~p~~~~~~~~~~~a~ni~tL~~~~e~~~~~~e~Ppe~vqDKI~FIiNNlS~~Nle~K~~Elke~L~~~y~~ 866 (2284)
.|++- -+ +-+...|.-++|+..+|+|.+||++..|+..|++|+|+.|+|.|.+
T Consensus 769 ------~fv~~-------~v--------------~c~~n~Eg~~~evV~~iLFaiNNl~~ln~n~ki~~lk~~Ltp~y~~ 821 (2005)
T COG5103 769 ------DFVRL-------IV--------------KCDANNEGRATEVVKSILFAINNLLDLNRNDKIHRLKEALTPGYVG 821 (2005)
T ss_pred ------hhhee-------Ee--------------ccccCccccHHHHHHHHHHHhhhHHhhhccchHHHHHHhcCccccc
Confidence 01110 00 0012244556777788999999999999999999999999999999
Q ss_pred hhhHHHHHhhcccCCchhHHHHHHHHHhCChhHHHHHHHHHHHHHHHHhcccccccChHHHHHHHhhhhhHhhhhhhcCc
Q 000087 867 WFAQYMVMKRASIEPNFHDLYLKFLDKVNSKALNREIVQATYENCKVLLGSELIKSSSEERSLLKNLGSWLGKLTIGRNQ 946 (2284)
Q Consensus 867 WFA~YLV~kRAsiEPNfH~LYl~fl~~l~~~~L~~~Vl~~Ty~~i~~LL~se~~~~ss~eRslLKNLGsWLG~iTLarNk 946 (2284)
||+.|||.+|++.|||||+||.++++.++++.||+.+.+.|.+.++.||+.... +.+|+++|||||+|||+|||||||
T Consensus 822 wfs~y~vtqR~~~e~n~~~ly~kvve~lgS~dly~~~~r~TL~~l~~ll~~~~e--s~~ekk~lKnLgswLG~ItLa~Nk 899 (2005)
T COG5103 822 WFSIYMVTQRSTAEENCRRLYGKVVERLGSKDLYLRFSRKTLEFLKMLLDYRCE--SPSEKKVLKNLGSWLGRITLAKNK 899 (2005)
T ss_pred ceeeEEEEeeccccchHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHhcccc--ChHHHHHHHHHHHHHhHHHHhhcC
Confidence 999999999999999999999999999999999999999999999999997644 889999999999999999999999
Q ss_pred ccccCCCChhHHHHHHHhcCceEEEechhhhhccccCCCccccCCCccHHHHHHHHHHHhcCCcccchhHHHHHHHHhhc
Q 000087 947 VLRAREIDPKSLIIEAYEKGLMIAVIPFTSKILEPCQSSLAYQPPNPWTMAILGLLAEIYSMPNLKMNLKFDIEVLFKNL 1026 (2284)
Q Consensus 947 PI~~k~ld~K~LL~eaY~~g~L~~VIPFV~KVLe~~~~S~vFkPPNPWtm~IL~lL~Ely~~~~LKlnLKFEIEVL~K~L 1026 (2284)
||+|+++|||++|+|||+.||+..|||||||||++++.|+||||||||+||||+||.|||+++++||+||||||+|+|+|
T Consensus 900 pIt~~q~~Fk~~lve~~~~~Ri~~vvpFV~k~L~~as~s~IFkPpNPW~mgILkLL~El~~~a~~~l~lkFEie~Ll~~l 979 (2005)
T COG5103 900 PITSEQFDFKKFLVESVECRRILFVVPFVSKFLRQASCSIIFKPPNPWVMGILKLLSELHSCAPRVLRLKFEIEGLLRHL 979 (2005)
T ss_pred ccccccccHHHHHHHHhhcCceEEeehHHHHHHHhcccceEecCCCchHHHHHHHHHHHHhcCcceeehhhhHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCccccccccccccchhh---ccCCCCCCCCCcCCCCCcccCCCCcCccCCCCCCCCCCCcCCCCCCCCCccccccccc
Q 000087 1027 GVDMKDITPTSLLKDRKRE---IEGNPDFSNKDVGASQPQLVPEVKPAIVSPLGHVDLPLDVASPPNSGGPTHLLSQYAA 1103 (2284)
Q Consensus 1027 ~ld~~dieps~~L~~r~~~---~~~~~d~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~q~~~ 1103 (2284)
|++++.|||++.++++... ++. ..|+. + ++ .+.|.+ ..+++||..
T Consensus 980 nv~~~~ikPs~~~~n~~V~ks~LEk---------------e~~Ed----v--L~-a~~~d~----------~~~~~qyi~ 1027 (2005)
T COG5103 980 NVELVPIKPSKSLGNHLVLKSRLEK---------------ELPED----V--LN-AKFPDG----------TDYLAQYII 1027 (2005)
T ss_pred ceeeccCChhhhhCcHHHHHHHHhh---------------hchHH----H--Hh-hhcccc----------chHHHHHHH
Confidence 9999999999999876531 110 01110 0 00 001100 012334331
Q ss_pred ccccCcCcchhHHHHhhccCCCCCCcccccccccCCCCCCCccccccCCCCCCccEeecccccccccchhhhhhHHHHHH
Q 000087 1104 PLRLSSGTLMEDEKLAALGISDQLPSAQGLFQASQSQSPFSVSQLSTPIPNIGTHVIINQKLTALGLHLHFQRVVPIAMD 1183 (2284)
Q Consensus 1104 ~~~~~~~~l~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~s~~~i~~~ip~l~~~~~i~~~l~~~~~~p~Lk~iV~~Aid 1183 (2284)
. + ++.++..+.. ..+...| -|.+|++.++|++
T Consensus 1028 ~----------~------------------------sSq~TvtD~v-------a~~~g~P-------~PaiK~~~Qlal~ 1059 (2005)
T COG5103 1028 E----------D------------------------SSQITVTDLV-------ARHVGSP-------KPAIKNLTQLALD 1059 (2005)
T ss_pred H----------h------------------------hhcchHHHHH-------HHHcCCC-------ChHHHHHHHHHHH
Confidence 0 0 0011111111 1111222 2899999999999
Q ss_pred HHHHhhhhhcchhhHHHHHHHHHHHHhhccCCChhhHHHHHHHHHHHHHHHhhhhHHHchHHHHHHHHHHHHHHhhcCCC
Q 000087 1184 RAIKEIVSGIVQRSVSIATQTTKELVLKDYAMESDETRIYNAAHLMVASLAGSLAHVTCKEPLRGSISSQLRNSLQGLTI 1263 (2284)
Q Consensus 1184 RAIrEII~PVVeRSVtIA~iTT~eLV~KDFA~E~DE~kmr~AAh~MVr~LAgSLAlVTckEPLr~si~~~Lr~~l~~~~~ 1263 (2284)
.+||||++.|||||+.||++||+.|++||||||.|++++..||++||++|||+||+|||+|||++.|.+++|++..++.+
T Consensus 1060 ~SVrEI~~aVVeks~gIAi~Tt~~l~~KDFa~ev~~s~l~~aar~Mv~~La~~La~vT~~EPlk~~i~~n~rs~a~~l~s 1139 (2005)
T COG5103 1060 LSVREICGAVVEKSCGIAIQTTMALFKKDFAMEVEKSMLYVAARNMVVNLAKFLALVTAQEPLKACISGNVRSYAMKLCS 1139 (2005)
T ss_pred HHHHHHHHHHHHHhccchhhHHHHHHHHHhhhccChhHHHHHHHHHHHHHHHHHHHHHhHhhHHHHHhccHHHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999888776
Q ss_pred cHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc-CCCCCcCcccccccccCCCCCCCCCC
Q 000087 1264 ASELLEQAVQLVTNDNLDLGCAVIEQAATDKAIQTIDGEIAQQLSLRRKHREG-VGSSFFDPNIYAQGSMGVPEALRPKP 1342 (2284)
Q Consensus 1264 ~~~~~Eq~i~~~vnDNldLac~iIEKaA~EKAi~eIDe~l~~~~~~RRkhre~-~g~~f~D~~~~s~~~~~LPepLr~kp 1342 (2284)
....+-+++..++++|++.||.+||||+++|++++|+..|+.++..||+||++ ++.||+|+++ +..+++||++|+++-
T Consensus 1140 v~~~~ae~vd~~~~eN~~va~~lIe~a~~~k~~~~i~aei~h~Iv~R~~Hrktt~n~PFvd~aa-a~~slnLps~L~ls~ 1218 (2005)
T COG5103 1140 VLDFSAEKVDKIAMENQDVACRLIERAGVSKVSESISAEIEHMIVERVRHRKTTPNLPFVDPAA-ANLSLNLPSSLELSI 1218 (2005)
T ss_pred hhhchHHHHHHHHHhchhHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhhccCCCCCccCccc-CccccCCCccccccc
Confidence 66778888999999999999999999999999999999999999999999998 7999999996 555788999999999
Q ss_pred CCCChhHHHhhhhhhcCcCCCCCCCCCCccccCccCCCCchhhhhhcccCCCCCCCCCCCCCCCCCcccccCCcccCCCC
Q 000087 1343 GHLSVSQQRVYEDFVRLPWQNQSSQGSHAMSAGSLTSSGDAAQASAYGLAGGQGNQGYSSSAGSTGFDAVSRPSDVASGT 1422 (2284)
Q Consensus 1343 gGl~~~Q~~VYEdF~r~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~ 1422 (2284)
||+||+|+++||||.|+|-..- ++|.+.++.-+ ....+++ ++++ -|.++...+
T Consensus 1219 ~~~Tpqqf~lyE~fD~l~ls~i---~~h~~~~~~n~----------~~Td~ad---------stda-----l~~nl~nt~ 1271 (2005)
T COG5103 1219 GKATPQQFSLYEDFDRLSLSTI---MGHIEKIAINA----------IDTDSAD---------STDA-----LNNNLNNTV 1271 (2005)
T ss_pred CCcCHHHhhhhhcccccccccc---ccccchhhhhh----------hcCChhh---------hhhh-----hccccchhh
Confidence 9999999999999999664221 22222211100 0000000 0000 000000000
Q ss_pred cccccccccccccccccCCCCCcccccccchhhccCChhhhhhhccCCCCCCCCCCCCCCCCCCCchhhhcccccccccc
Q 000087 1423 TESTSAGFLSTSLVHIGAADGGILHNSESESVNAAFTPAATELYAADSTEPVKEPGASSQSLPSTAAPERIGSSILEPSL 1502 (2284)
Q Consensus 1423 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 1502 (2284)
...++|. +.++... ... . +. ...+. ..+++.. .+..+.
T Consensus 1272 --e~eAnQt---a~~yq~n------------~L~-i-~~--ql~Ql------------~~~~Py~-~~~~V~-------- 1309 (2005)
T COG5103 1272 --ENEANQT---ALEYQEN------------LLI-I-KA--QLVQL------------SKKIPYS-SKKNVI-------- 1309 (2005)
T ss_pred --hhHHHHH---HHHHHHH------------hhh-h-hh--HHHHh------------cccCCcc-hhhcCc--------
Confidence 0000000 0000000 000 0 00 00000 0011111 011111
Q ss_pred chhhhhHHHHHHHHHHHHHhhcCCcchhHHHHHhhhHHHHHhhcChhHHHHHHHHHHHHHHhcccCCcchHHHHHHHHHH
Q 000087 1503 QTRDALDKYHIVAQKLDALIGNDAREAEVQGVISEVPEIILRCISRDEAALAVAQKVFKGLYENASNNLHFSAHLAILAA 1582 (2284)
Q Consensus 1503 ~~~~~le~~~~~~~~l~~l~~~~~~~~~i~~~i~~v~~~i~~~~~rd~~al~~aqki~~~L~~~~~~~l~~ev~~~~L~~ 1582 (2284)
. +..|-. +.+ +. +++..++.+|...|.++ |+.++.++|.+++.|+..+.+++++||+.++||+
T Consensus 1310 -a----D~e~~~---lkE-----~~-NQ~~t~~~~Il~~Ia~s---d~~~l~c~q~c~~il~~~skSp~~~evls~~lEk 1372 (2005)
T COG5103 1310 -A----DEEHGL---LKE-----GK-NQFETVFRRILESIASS---DDKDLECIQLCRYILGHLSKSPSKEEVLSRCLEK 1372 (2005)
T ss_pred -c----hhhhhH---HHh-----hH-HHHHHHHHHHHHHhccc---hhhHHHHHHHHHHHHhccccCchHHHHHHHHHHH
Confidence 0 111111 111 11 35667777777777665 8999999999999999999999999999999999
Q ss_pred HHHHhHHHHHHHHHhhhccccccccCHHHHHHHHHhCCCChhhHHHHHHHHHhcCCChhhHHHHHHHHHHHhcCCcchh-
Q 000087 1583 IRDVCKLVVKELTSWVIYSDEERKFNRDITMGLIRSELLNLAEYNVHMAKLIDGGRNKAATEFAISLLQTLVTDESRVV- 1661 (2284)
Q Consensus 1583 L~~~~~~~~kevt~wl~~~~d~rk~N~~vi~~Lir~~Li~~~e~D~~Lak~i~~~~n~~av~Fa~~Ll~~~l~~~~~~~- 1661 (2284)
||++|-+++|+|.||++|+.|.||||+|+|.+||++||||..|||.+|++.|.+.. ..++|||+.|++.++.+|.++.
T Consensus 1373 ic~~S~kt~k~V~~wl~ysnD~rKfnip~I~slie~nli~~~E~D~~l~r~i~~~~-gnvtdFai~Ll~~~V~~e~pi~~ 1451 (2005)
T COG5103 1373 ICKISFKTQKEVLGWLIYSNDPRKFNIPLIGSLIEHNLINVVEYDQALSRKIPLAD-GNVTDFAIALLASLVTAEVPICT 1451 (2005)
T ss_pred HHhHhHHHhhhhheeeeecCChhhcCcHHHHHHHHhccchhhhHHHHHHhhccccc-cchHHHHHHHHHHHhccCCceee
Confidence 99999999999999999999999999999999999999999999999999997644 4479999999999888887665
Q ss_pred hhhHHHHHHHHHHHHcCCCChhHHHHHHHHHhCcccccCCCCCCccccchhhhhhcccccccCcccCCCCCCCCCCCCCC
Q 000087 1662 ISELHNLVDALAKLAAKPGSPESLQQLIEIVRNPAANANASSGATTAKDDKARQSKDKKAYSHTTANREDYNIPESVDPD 1741 (2284)
Q Consensus 1662 ~~df~~tleaL~~~~~~~~~~~~~~~l~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d 1741 (2284)
..||.+|+|.|+.-. + +.++++.+++.+... . .+.. ..
T Consensus 1452 ~~dFI~tLe~la~s~----d-~~vk~f~~~~~~tm~------------~---------~v~k----------------gn 1489 (2005)
T COG5103 1452 VYDFICTLEMLAGSS----D-PKVKDFFQKISNTMM------------H---------IVAK----------------GN 1489 (2005)
T ss_pred HHHHHHHHHHHhccC----C-hhHHHHHHHHHHhhh------------h---------cccc----------------cc
Confidence 489999999886432 2 455777766643100 0 0000 11
Q ss_pred CCChHHHHHHHHHHHHHhhcCCCCCchHHHHHHHHHHHcCcccCCchhHHHHHHHHHHHHHHhhhccccCCCCCCCCCcc
Q 000087 1742 PVGFPEQVSMLFAEWYQICELPGSNDAACTRYVLQLHQNGLLKGDDMTDRFFRRLTEVSVAHCLSSEVINPGTLQSPQQS 1821 (2284)
Q Consensus 1742 ~~~~~eq~~~lF~EWv~l~~~~~~~~~~~~~Fi~qL~~~giL~~~d~~~~FfR~~~E~sV~~~~~~~~~~~g~~~~~~~~ 1821 (2284)
...+.||+..+|.|||++.++...+|..-..|+.||+++|+++..|+...|||+.+|.+|..|.+.. +
T Consensus 1490 Kqq~ndqi~iVf~ewv~llrn~~~nD~v~~~F~~ql~e~g~~s~~~~~~~ffk~sle~~i~aF~e~~------------p 1557 (2005)
T COG5103 1490 KQQLNDQIIIVFSEWVELLRNCRFNDTVPEMFLPQLMERGDYSASLDIRSFFKVSLEHFIRAFHERI------------P 1557 (2005)
T ss_pred cccccceEEEeeHHHHHHHHhcccccccHHHHHHHHHHccCCCchHHHHHHHHhhHHHHHHHHhhcC------------C
Confidence 2356789999999999999999999999999999999999999999999999999999999997432 2
Q ss_pred ccccchhhHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhcCCCCCchHHHHHHHHHhhcCCCCCCC
Q 000087 1822 QSLSFLAIDIYAKLMLSILKCCPVEQGSSKIFLLSKILTVTVKFILKDAEEKKASFNPRPYFRLFINWLLDMSSLDPVAD 1901 (2284)
Q Consensus 1822 ~~~~f~~iDA~akLi~~lvk~~~~~~~~~k~~~L~kiL~iiv~vl~~dhe~~~~~FnqrpyfRlfs~LL~el~~~d~~l~ 1901 (2284)
.+.+|..||||+.||+.++++. +..+.++..|++||++.+++|+.++|..+++.||+|+||||||++|.||.......+
T Consensus 1558 ta~~y~~IDal~sLi~n~l~~e-G~te~T~s~~~~kii~~i~~VFae~h~~~~e~~h~~~fFrLfS~il~e~~dv~~~d~ 1636 (2005)
T COG5103 1558 TAYCYLKIDALPSLIKNRLYEE-GSTEGTVSVLFRKIIKDILFVFAEAHRKRAEFVHNYLFFRLFSRILIETLDVIDEDT 1636 (2005)
T ss_pred cccceeeccchHHHHHHHHHHh-ccccchHHHHHHHHHHHHHHHHHHHHHHhhhhhhcccHHHHHHHHHHHHhhhhhccc
Confidence 4789999999999999999995 455567889999999999999999999999999999999999999999977543444
Q ss_pred cchHHHHHHHHHHhhhcCCCCCCchhhHHhHHhhcccchHHhhcCCCCCChHHHHHHHHHHHHhhhhhhcCCCCCchHHH
Q 000087 1902 GSNFQILSAFANAFHVLQPLKVPAFSFAWLELVSHRSFMPKLLIGNGQKGWPYIQRLLVNLLQFLEPFLRNAELGVPVRF 1981 (2284)
Q Consensus 1902 ~~~~~il~~fa~~l~~LqP~~~PgF~FaWl~LISHR~FmP~lL~~~~~~GW~~~~~LL~~ll~Fl~~~L~~~~l~~~i~~ 1981 (2284)
+.-..+.+.|-++|..|||.+||||+|||++|+|||+.+|++|+.|+.+||..|..+|+++|||+. ++...+...+++
T Consensus 1637 s~fv~~~Sv~y~~f~alqP~~fPgFtfawl~llSH~~llP~vL~v~Nd~~~d~f~~~lmsflKFlD--~s~~~v~~~~~~ 1714 (2005)
T COG5103 1637 SCFVNNRSVVYSIFEALQPSRFPGFTFAWLELLSHKFLLPKVLLVNNDKINDLFSEGLMSFLKFLD--LSEEGVVLVMEA 1714 (2005)
T ss_pred hhhhhhHHHHHHHHHHcCcccCCchHHHHHHHHHhhhhhhhhhhccchhhHHHHHHHHHHHHHHhc--chHHHHHHHHHH
Confidence 555678889999999999999999999999999999999999999999999999999999999998 788888899999
Q ss_pred HhHhHHHHHHHHHhcchhHHHHHhHhhhccCCCCCccccceeecccCCCCCCCCCCCCCCCCCCCcCcCCCCccccchHH
Q 000087 1982 LYKGTLRVLLVLLHDFPEFLCDYHFTFCDVIPPSCIQMRNIILSAFPRNMRLPDPSTPNLKIDLLPEIRDPPRIFSEVDA 2061 (2284)
Q Consensus 1982 lYkGtLRilLvLlHDfPEFL~~yh~~lc~~IP~~ciQLRNlILSA~P~~mrLPDPftp~Lkvd~LpEi~~~P~i~~d~~~ 2061 (2284)
+|+|+||+.||++||||-||+++||++...+|+.|+||||+||||||++|.+||||..||||.++|+|+..|.++.|...
T Consensus 1715 ly~Gflr~iLv~~hD~P~FLit~~yql~~~~P~e~vqlrNm~lSa~Psdlt~p~Pfa~~Lkv~~~P~~k~~p~~f~d~~v 1794 (2005)
T COG5103 1715 LYCGFLRTILVYLHDFPGFLITQIYQLFRRNPLECVQLRNMMLSAYPSDLTYPCPFAQGLKVQEYPHIKNFPNQFRDRIV 1794 (2005)
T ss_pred HHhcchheeeeeeccCchHHHHHHHHHhhcCCHHHHHHHHHHHHhccccCcCCCchhcccccccChHhhhhhHHhccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred HHHHhhhhHHHHHHhccCCCCccHHHHHHHHccCCccccccCCcc---ccHhHHHHHHHHHHHHHHHhhhcccCCccccC
Q 000087 2062 ALRAKQMRADVDDYLKTGQPGSSFLSELKQKLLLPPSEAASAGTR---YNVPLINSLVLYVGMQAIHQLQTRTSHAQSTG 2138 (2284)
Q Consensus 2062 ~L~~~~lk~~vD~yL~~r~~~~~~l~~l~~~L~~~~~~~~~~G~~---yN~~liNAlVLyVG~~Ai~~~~~~~~~~~~~~ 2138 (2284)
.| .++++.+| | |.+..+.+..+.+++...-+.....|.. ++-..+-++|+|+|+.++... .+
T Consensus 1795 ~l--e~~~s~~d--L--e~~~~S~l~~~~s~~~~d~y~~k~t~~~~~~~dn~~~~~~V~h~~~es~~~~-----~~---- 1859 (2005)
T COG5103 1795 PL--EGQNSFFD--L--EACLRSALQNRTSVKVTDLYIGKNTPLWVYLIDNLNEMDAVSHTVVESIKFM-----IE---- 1859 (2005)
T ss_pred ch--hhcccchh--h--HHHhhhhhhHHHHHHHHHhhccccCceeeeeeccHHHHHHHHHHHhhhHHHH-----HH----
Confidence 87 47888888 5 5566677777777665543333233322 245678899999999985532 11
Q ss_pred CCCchhhhh-hhhHHHHHHHHHhccChhhHHHHHHHHHhhhcCCChhhHHHHHHHHHHhhccc----chhhHHHHHHHHH
Q 000087 2139 NNSSLTAFL-VSAALDIFQTLIQDLDTEGRYLFLNAAANQLRYPNNHTHYFSFVLLYLYAEAN----QEIIQEQITRVLF 2213 (2284)
Q Consensus 2139 ~~~~~~~f~-~s~~~~il~~L~~~ld~EgRY~ll~aiaNqLRYPN~HT~~FS~~lL~LF~~~~----~~~IqEqItRVLL 2213 (2284)
.|+ +++.+.++..++..++++.||+++.||++||||||+||+||||++|++|.+++ +-.||||||||||
T Consensus 1860 ------~f~~ks~~~t~l~~~~r~g~~~~rY~ll~ai~~qlRYp~ihTy~fs~vfl~~fkS~~~N~QkL~ikE~m~t~lL 1933 (2005)
T COG5103 1860 ------RFMHKSEILTMLWIRMRAGGPPKRYFLLTAILAQLRYPEIHTYDFSRVFLKSFKSHGYNPQKLLIKEQMTTVLL 1933 (2005)
T ss_pred ------HHhccccHHHHHHHHHhcCCCchhhHHHHHHHHHhcCCCcchhHHHHHHHHHHhhcCCChHHHHHHHHHHHHHH
Confidence 233 36689999999999999999999999999999999999999999999998763 4579999999999
Q ss_pred HHhccCCCCChHHHHHHHHHhhCCCCccccCCcCcchHHHHHHHHHHHHhcCCCCCCC
Q 000087 2214 ERLIVNRPHPWGLLITFIELIKNPRYNFWNQSFIRCAPEIEKLFESVARSCGGLKPVD 2271 (2284)
Q Consensus 2214 ERlIv~rPHPWGLliTFiELikNp~Y~Fw~~~Fv~~aPEIe~lF~svarsc~~~~~~~ 2271 (2284)
||+||||||||||+|||+||+||.+||||+||||+..|||.++|+++.+++|.+..+.
T Consensus 1934 eRII~NrPH~WGl~i~FTeLlkNeD~Nf~k~Pyikr~~EI~~lfdsL~e~v~a~ssan 1991 (2005)
T COG5103 1934 ERIICNRPHPWGLLITFTELLKNEDYNFWKHPYIKRNDEICRLFDSLHEHVMAPSSAN 1991 (2005)
T ss_pred HHHHcCCCCcchhheeHHHHhcccccchhcCcccccCHHHHHHHHHHHHHhhCccccc
Confidence 9999999999999999999999999999999999999999999999999999876544
No 2
>KOG1831 consensus Negative regulator of transcription [Transcription]
Probab=100.00 E-value=3.4e-291 Score=2711.38 Aligned_cols=1470 Identities=37% Similarity=0.591 Sum_probs=1165.6
Q ss_pred hhhhhhhcccCchhHHHHHHHhhcccccCHHHHHHHHhhcCcchHHHHHHHHHHHHhhcccccccCCCCCCCcccccccc
Q 000087 395 KILSSVLEMIPSPFAIRLAVIASQKELVDLEKWLSINLSTYKDVFFEECLKFVKEVQFGRSQDFSAQPFHHSGALLNLYM 474 (2284)
Q Consensus 395 k~L~~lL~~~p~~f~idLA~lAsrre~l~lekWl~~~l~~~~~~f~~a~l~FL~~k~~~~~~~~~~~~~~~~~~~~~L~~ 474 (2284)
.-++.|.|+.||.++++.+.+|+.++++++..|+..++.--.+ |..++.-... .++.++.+..+...
T Consensus 82 ~~~~~v~Nm~pn~~~~n~~~la~~~~a~~F~~~l~~~~~~~~~-----~~~~~s~~~~--------~~q~~~~~~~~~~~ 148 (1591)
T KOG1831|consen 82 PGMDIVGNMSPNLEALNIRDLASCFGAVNFSIWLLESLYLMID-----DAVPLSLIIT--------APQEPSFKPWPNER 148 (1591)
T ss_pred CcchhhhhcCcchhhhchHhhhhhcCCCCchhhhcccceeecc-----CCCcccceee--------ccccccCCCChhHH
Confidence 4578899999999999999999999999999999988653221 1222211111 01111111111100
Q ss_pred -hhHHHHHHHHHhhhCCCCchHHHHHHHHHHHHhhccCCCCCCCCCCCC-----CCCCCCchhHHHHHHHHHHHhhccCC
Q 000087 475 -EKIPVILKLLKAHIGLITSTKLSEEIEKFQAVVLDSTPRLQNGEAADS-----STSEGYADDIEAEANSYFHQMFSGQL 548 (2284)
Q Consensus 475 -etv~~lL~~L~~~~~~~~s~~l~e~l~~~~~~~i~~~PrL~n~~~~d~-----~~~~~~~~dIE~Ean~yfqkmYs~ei 548 (2284)
.++..++-.... + ++-.+..-++|.+|. .+..+|++|||+|||+||||||+ .+
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 112221111100 0 111122224555664 24578999999999999999999 99
Q ss_pred CHHHHHHHHHHhhcCCcccchhhHHhHHHhhhhhhccCCCCcHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHHhcC
Q 000087 549 TIEAMVQMLARFKESSVKREHSIFECMIGNLFEEYRFFPKYPERQLRIAAVLFGSIIKHQLVTHLTLGIALRGVLDALRK 628 (2284)
Q Consensus 549 sI~~iv~~L~r~K~S~~~rdqdiFaCMIh~LFdEYrFf~~YP~~eL~iTAvLFG~lI~~~Lv~~~~L~iALr~ILeAlrk 628 (2284)
+|+++|++|+|||.|.++|||++|+||.|+||||||||++||++||++||+||||||.|+|+++.+||+|+|+|++|+++
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 CCCCcccchHHHHHHHHHHhhhhhhHHHHHHhcccccccccHHHHHHHHHHHHhhccCCCCCCCCCCCcccccccccccC
Q 000087 629 PADSKMFVFGTKALEQFVDRLIEWPQYCNHILQISHLRSTHAELVAFIERALARISSGHLESDGASNPAAHQHVSSQATS 708 (2284)
Q Consensus 629 p~~SkMf~FGiqAL~qF~~RL~EwPqyC~~Ll~ip~L~~~~p~l~~~ie~~l~~~~~~~~~~~~~~~~~~~q~~~~q~~~ 708 (2284)
||+||||+||++||.+|+.||.+||+||.+|+.+|++...+|++|++|.+..- +. +. +.
T Consensus 288 P~~skl~~Fgv~Al~~frskL~~Yp~yC~~Il~~~~~s~~~~~l~~~I~~~~~---sa----na---~~----------- 346 (1591)
T KOG1831|consen 288 PPSSKLFIFGVQALLPFRSKLLDYPKYCFDILSIPPFSKFRPHLYDSIWETAT---SA----NA---TT----------- 346 (1591)
T ss_pred CChhHHHHHHHHHHHHHHHHhcchHHHHHHHHhCcchhhccHHHHHHHHhhhh---hc----cC---CC-----------
Confidence 99999999999999999999999999999999999999999999999977421 11 00 00
Q ss_pred CCCCccCCcccccccchhhHHHhhhcccccccccccccccccCCCCCCcccCC-CCCCcCCCCCCchhhhhcccCCCccc
Q 000087 709 GNGEVSGSGITQLGQQLSSQIQLQQRSESVVDDRHKVSAASSSDMKPLLSSIG-QPSSVAPLGDTSSAQKLHNAVSAPAM 787 (2284)
Q Consensus 709 ~~~~~~~~~~~~~~~~~~~~~~~qq~~~~~l~~~~~~~~~~~~~~~p~~~s~~-~~~~~~~~~~~~~~~~~~~~p~~~~~ 787 (2284)
.+ ..|..+..+ .++.+
T Consensus 347 -----~~-------------------------------------s~pv~~~~p~~~~av--------------------- 363 (1591)
T KOG1831|consen 347 -----RK-------------------------------------SDPVRSASPYLDSAV--------------------- 363 (1591)
T ss_pred -----cc-------------------------------------cccchhccccccccc---------------------
Confidence 00 000000000 00000
Q ss_pred cccCCCccCCCCCccccccccccchHHHHHHhhhcCCCCCCCChhhhHhHhhhhhcCCcccHHHHHHHHHHHhhhcchhh
Q 000087 788 LSISSGFARPSRGVTSTKFGSALNIETLVAAAERRETPIEAPASEVQDKISFIINNISALNVEAKAKEFTEILKEQYYPW 867 (2284)
Q Consensus 788 ~~~~~~~~~p~~~~~~~~~~~a~ni~tL~~~~e~~~~~~e~Ppe~vqDKI~FIiNNlS~~Nle~K~~Elke~L~~~y~~W 867 (2284)
+. ..+ ..+.+.|||+|+|||+|++||+|+.|+.+|++|+|++|+++||+|
T Consensus 364 -s~----~~~-------------------------P~n~~~~~e~v~dkilF~lNNlsq~N~~qKvdevk~~ltp~y~~W 413 (1591)
T KOG1831|consen 364 -SK----HVE-------------------------PKNAEGPPEDVVDKILFPLNNLSQLNFNQKVDEVKEILTPEYYPW 413 (1591)
T ss_pred -cc----cCC-------------------------cccccCCchhhhhhheeeechHhhhhhHHHHHHHHHHcChhhHHH
Confidence 00 001 112358999999999999999999999999999999999999999
Q ss_pred hhHHHHHhhcccCCchhHHHHHHHHHhCChhHHHHHHHHHHHHHHHHhcccccccChHHHHHHHhhhhhHhhhhhhcCcc
Q 000087 868 FAQYMVMKRASIEPNFHDLYLKFLDKVNSKALNREIVQATYENCKVLLGSELIKSSSEERSLLKNLGSWLGKLTIGRNQV 947 (2284)
Q Consensus 868 FA~YLV~kRAsiEPNfH~LYl~fl~~l~~~~L~~~Vl~~Ty~~i~~LL~se~~~~ss~eRslLKNLGsWLG~iTLarNkP 947 (2284)
||+|+|+||||+|+|||+||.+|++.+++.. | -+||++|||||||||.||||||||
T Consensus 414 fs~YiV~qR~S~E~Nf~~LYskFi~ai~n~~--------t----------------~~dk~~LKNLgsWLG~iTl~rNkP 469 (1591)
T KOG1831|consen 414 FSQYIVTQRVSKEINFHELYSKFISAIKNSV--------T----------------ESDKRLLKNLGSWLGEITLGRNKP 469 (1591)
T ss_pred HHHHHhhhhhhcccchHHHHHHHHHHHhCcc--------c----------------hhHHHHHHHHHHHHHHHHHhcCCc
Confidence 9999999999999999999999999999982 2 179999999999999999999999
Q ss_pred cccCCCChhHHHHHHHhcCceEEEechhhhhccccCCCccccCCCccHHHHHHHHHHHhcCCcccchhHHHHHHHHhhcC
Q 000087 948 LRAREIDPKSLIIEAYEKGLMIAVIPFTSKILEPCQSSLAYQPPNPWTMAILGLLAEIYSMPNLKMNLKFDIEVLFKNLG 1027 (2284)
Q Consensus 948 I~~k~ld~K~LL~eaY~~g~L~~VIPFV~KVLe~~~~S~vFkPPNPWtm~IL~lL~Ely~~~~LKlnLKFEIEVL~K~L~ 1027 (2284)
|++.++|||+||+|||.+|++..|+|||||||+.|.+|+|||||||||||||++|+|+|+.||||+|||||||||||+||
T Consensus 470 I~~l~l~~kslLlEaY~sg~ll~VvPFVaKIL~~asksrIFkpPnpW~~gIlklL~ELh~e~d~klnLkFEIEVLlkslN 549 (1591)
T KOG1831|consen 470 IKELDLDFKSLLLEAYGSGRLLPVVPFVAKILEGASKSRIFKPPNPWTMGILKLLAELHQEADLKLNLKFEIEVLLKSLN 549 (1591)
T ss_pred hHHhhhhHHHHHHHHhccCceeecchHHHHHHHhhhhccccCCCCchHHHHHHHHHHhcccccceeeeeeeeeehhcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccccccccccccchhhccCCCCCCCCCcCCCCCcccCCCCcCccCCCCCCCCCCCcCCCCCCCCCccccccccccccc
Q 000087 1028 VDMKDITPTSLLKDRKREIEGNPDFSNKDVGASQPQLVPEVKPAIVSPLGHVDLPLDVASPPNSGGPTHLLSQYAAPLRL 1107 (2284)
Q Consensus 1028 ld~~dieps~~L~~r~~~~~~~~d~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~q~~~~~~~ 1107 (2284)
++++++||+++++|..+. .+... .+.++.. +..+++.. +|
T Consensus 550 ~~l~~le~~~~lnn~~~i-~~~L~-----------~~~~e~h-------~~~~~~~~--------------q~------- 589 (1591)
T KOG1831|consen 550 VILSELEPSETLNNIIRI-KKQLV-----------LMKLETH-------QSLELEDI--------------QQ------- 589 (1591)
T ss_pred chHhhcchhhHHhhHHhH-HHHHc-----------cCChhhc-------cccccCch--------------hc-------
Confidence 999999999999994431 11110 0000000 00000000 00
Q ss_pred CcCcchhHHHHhhccCCCCCCcccccccccCCCCCCCcccccc-CCCCCCccEeecccccccccchhhhhhHHHHHHHHH
Q 000087 1108 SSGTLMEDEKLAALGISDQLPSAQGLFQASQSQSPFSVSQLST-PIPNIGTHVIINQKLTALGLHLHFQRVVPIAMDRAI 1186 (2284)
Q Consensus 1108 ~~~~l~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~s~~~i~~-~ip~l~~~~~i~~~l~~~~~~p~Lk~iV~~AidRAI 1186 (2284)
+++. + ...|++++... +..++.+++...| ||++|++|+.|++++|
T Consensus 590 ----------------------~~~~---~--~~~fa~~~~n~~t~~~~i~~l~~~~-------~P~~Kh~~~~Aleqsv 635 (1591)
T KOG1831|consen 590 ----------------------VTLG---N--TIAFAYDARNVSTATEVIKQLDLRP-------HPDIKHRVQEALEQSV 635 (1591)
T ss_pred ----------------------cccc---C--CccceecccccchhhhhhhhccCCC-------CccHHHHHHHHHHHHH
Confidence 0000 0 01144444321 1122333344443 8999999999999999
Q ss_pred HhhhhhcchhhHHHHHHHHHHHHhhccCCChhhHHHHHHHHHHHHHHHhhhhHHHchHHHHHHHHHHHHHHhhcCCCcHH
Q 000087 1187 KEIVSGIVQRSVSIATQTTKELVLKDYAMESDETRIYNAAHLMVASLAGSLAHVTCKEPLRGSISSQLRNSLQGLTIASE 1266 (2284)
Q Consensus 1187 rEII~PVVeRSVtIA~iTT~eLV~KDFA~E~DE~kmr~AAh~MVr~LAgSLAlVTckEPLr~si~~~Lr~~l~~~~~~~~ 1266 (2284)
+|||.||||||+.||++||+.||+||||+|+||+|||.||+.|||+||++||++||||||+++|+++|+..+.++.....
T Consensus 636 ~eii~~Vv~rs~~IA~ttTe~lirKDFA~e~~es~l~~Aa~~M~r~la~~lAmiTcreplk~am~~nl~~~~~~~l~~~~ 715 (1591)
T KOG1831|consen 636 VEIIEPVVERSSGIASTTTESLIRKDFALERDESRLRLAASQMVRELAAGLAMITCREPLKVAMSSNLVLAALSLLSLMA 715 (1591)
T ss_pred HHHHHHHHHHhhceeehhHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHhhHHHHHhhhhHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999877666788
Q ss_pred HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc-CCCCCcCcccccccccCCCCCCCCCCCCC
Q 000087 1267 LLEQAVQLVTNDNLDLGCAVIEQAATDKAIQTIDGEIAQQLSLRRKHREG-VGSSFFDPNIYAQGSMGVPEALRPKPGHL 1345 (2284)
Q Consensus 1267 ~~Eq~i~~~vnDNldLac~iIEKaA~EKAi~eIDe~l~~~~~~RRkhre~-~g~~f~D~~~~s~~~~~LPepLr~kpgGl 1345 (2284)
.+++++..+++||++++|++|||+|+|||+.|||.+|++++..|+.||++ ++.+|+|+....+. ..|||++|+++||+
T Consensus 716 ai~~a~~t~~~dNv~l~~~~Iek~a~eka~~dI~~~L~q~~~~Rv~~k~~~~~~~fvD~~~~~~~-~~LP~~vr~~~~~~ 794 (1591)
T KOG1831|consen 716 AIARAADTLQSDNVELVVKFIEKTAIEKATQDIDSRLEQDICGRVFHKENPEVMPFVDLLSAAYS-CTLPEVVRLKIGGL 794 (1591)
T ss_pred HHHHHHHHHHhhchhhHhhhhHHHHHHHHHHHHHHHHHHhhHhheecccCCccccchhhhhhhhh-ccCcHhhhcccCCC
Confidence 99999999999999999999999999999999999999999999999997 69999999875654 44999999999999
Q ss_pred ChhHHHhhhhhhc-CcCC-CCCCCCCCccccCccCCCCchhhhhhcccCCCCCCCCCCCCCCCCCcccccCCcccCCCCc
Q 000087 1346 SVSQQRVYEDFVR-LPWQ-NQSSQGSHAMSAGSLTSSGDAAQASAYGLAGGQGNQGYSSSAGSTGFDAVSRPSDVASGTT 1423 (2284)
Q Consensus 1346 ~~~Q~~VYEdF~r-~p~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~ 1423 (2284)
+|+|++|||+|+| +|+. ..++...+... ++++.++.+.-.
T Consensus 795 ~~~l~~vYe~F~k~i~~~~~~s~~~~la~~--------------------------------------~~~~~dlt~~~~ 836 (1591)
T KOG1831|consen 795 TPQLFRVYEEFPKPIPGFLGNSSRKDLAEY--------------------------------------ITESSDLTQPHV 836 (1591)
T ss_pred CHHHHHHHHHcccccccccccCCCcccccc--------------------------------------cCCCccccchhh
Confidence 9999999999998 5541 11111111100 011111111000
Q ss_pred ccccccccccccccccCCCCCcccccccchhhc-cCChhhhhhhccCCCCCCCCCCCCCCCCCCCchhhhcccccccccc
Q 000087 1424 ESTSAGFLSTSLVHIGAADGGILHNSESESVNA-AFTPAATELYAADSTEPVKEPGASSQSLPSTAAPERIGSSILEPSL 1502 (2284)
Q Consensus 1424 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 1502 (2284)
.+ ..+.....++. ++ .... .+..++...++.. +++ ....++.+
T Consensus 837 ~s---~~~~lv~~ei~----------~~-~~~~a~~~~i~~~~l~~~----------a~s---~~~~m~~v--------- 880 (1591)
T KOG1831|consen 837 IS---NALDLVVREIC----------GA-IVEKACQTAIQTGMLQFK----------AQS---VEKLMEEV--------- 880 (1591)
T ss_pred hh---HHHHHHHHHHH----------HH-HHHHHHHHHHHhhhhhhh----------hhc---chhhHHhc---------
Confidence 00 00000000000 00 0000 0000000000000 000 00011111
Q ss_pred chhhhhHHHHHHHHHHHHHhhcCCcchhHHHHHhhhHHHHHhhcChhHHHHHHHH--HHHHHHhcccCCcchHHHHHHHH
Q 000087 1503 QTRDALDKYHIVAQKLDALIGNDAREAEVQGVISEVPEIILRCISRDEAALAVAQ--KVFKGLYENASNNLHFSAHLAIL 1580 (2284)
Q Consensus 1503 ~~~~~le~~~~~~~~l~~l~~~~~~~~~i~~~i~~v~~~i~~~~~rd~~al~~aq--ki~~~L~~~~~~~l~~ev~~~~L 1580 (2284)
+.++..............++.. .-..-.+.+ +.+...+ ..+--.+++..+|
T Consensus 881 -----------------------~~~~~~~~~~~~~~~~~ar~i~-hli~~~V~~~~~~l~~~~---~~~~I~~i~m~iL 933 (1591)
T KOG1831|consen 881 -----------------------PARNMVVNLVNSLLLLVARSIE-HLISGLVSYFMKNLELDF---STEKIFKIIMEIL 933 (1591)
T ss_pred -----------------------cchhhhHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHhh---cchhHHHHHHHHH
Confidence 1111111111111111111000 000011111 1111111 1122345777888
Q ss_pred HHHHHHhHH-HHHHHHHhhhccccccccCHHHHHHHHHhCCCChhhHHHHHHHHHhcCCChhhHHHHHHHHHHHhcCCcc
Q 000087 1581 AAIRDVCKL-VVKELTSWVIYSDEERKFNRDITMGLIRSELLNLAEYNVHMAKLIDGGRNKAATEFAISLLQTLVTDESR 1659 (2284)
Q Consensus 1581 ~~L~~~~~~-~~kevt~wl~~~~d~rk~N~~vi~~Lir~~Li~~~e~D~~Lak~i~~~~n~~av~Fa~~Ll~~~l~~~~~ 1659 (2284)
+-+|....+ ..+.|+-.+..+++++|||++.+..|++.+|++..++|.+|+++|++|.|..++.|+++|++....++..
T Consensus 934 ~~ic~~~qk~~~~~vs~a~s~~~~~~e~n~~~~~~L~~~~l~~~~~vd~~l~~amDs~~n~~vi~f~iell~~~~~~dnv 1013 (1591)
T KOG1831|consen 934 DNICRFIQKAGVRKVSEAISSSRSSLEYNIEKAEHLILSLLLDSGHVDKHLAKAMDSGGNQEVIAFLIELLRIAYGGDNV 1013 (1591)
T ss_pred HHHHHhccHHHHHHHHHHHHhchHHHHhhHHHHHHHHHHhccChhhHHHHHHHHhccCCChHHHHHHHHHHHHhccCcch
Confidence 888988744 5556888888999999999999999999999999999999999999999999999999999999988885
Q ss_pred hhh-h--hHHHHHHHHHHHHcCCCCh----hHHH----HHHHHHhCcccccCCCCCCccccchhhhhhcccccccCcccC
Q 000087 1660 VVI-S--ELHNLVDALAKLAAKPGSP----ESLQ----QLIEIVRNPAANANASSGATTAKDDKARQSKDKKAYSHTTAN 1728 (2284)
Q Consensus 1660 ~~~-~--df~~tleaL~~~~~~~~~~----~~~~----~l~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1728 (2284)
+.. . .|..|.|.+.|+.+.-.+. +... ..++.+-. ++.+
T Consensus 1014 i~~~~~~~~~~t~E~~~ri~q~v~s~~~~~g~~~~~~~~~v~~~~k----------------------------~~s~-- 1063 (1591)
T KOG1831|consen 1014 IADEWKNLFKETKEELFRILQSVESSEDKSGECASLCDYIVEHAIK----------------------------SGSS-- 1063 (1591)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHhcccccchhhhhHHHHHHHhccC----------------------------CCCc--
Confidence 433 3 5778999998865321111 1111 11111110 0000
Q ss_pred CCCCCCCCCCCCCCCChHHHHHHHHHHHHHhhcCCCCCchHHHHHHHHHHHcCcccCCchhHHHHHHHHHHHHHHhhhcc
Q 000087 1729 REDYNIPESVDPDPVGFPEQVSMLFAEWYQICELPGSNDAACTRYVLQLHQNGLLKGDDMTDRFFRRLTEVSVAHCLSSE 1808 (2284)
Q Consensus 1729 ~~~~~~~~~~~~d~~~~~eq~~~lF~EWv~l~~~~~~~~~~~~~Fi~qL~~~giL~~~d~~~~FfR~~~E~sV~~~~~~~ 1808 (2284)
...-....+|+.++.||++.+|.|||++|+.+..++....+||+||+++|||++||..++|||.|+|+||+.++...
T Consensus 1064 ---~~~m~~~~~~~~~lt~K~~~v~~~Wv~L~~~~~~~~~s~~~fi~ql~~~GVls~dd~ltqFfr~~~el~~~i~~~a~ 1140 (1591)
T KOG1831|consen 1064 ---ADFMFRRMDDKQKLTEKTEIVFLEWVILLNDSRKNDESLAAFIQQLNEIGVLSTDDLLTQFFRADLELCVVIFLEAS 1140 (1591)
T ss_pred ---hhHHHHhcCcchhhhhHHHHHHHHHHHHHhccccchHHHHHHHHHHHHcCcccchHHHHHHHHhhhhhhHHHHHHhc
Confidence 00001224577899999999999999999999999999999999999999999999999999999999999998543
Q ss_pred ccCCCCCCCCCccccccc-hhhHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhhhhhhhcCCCCCchHHHHH
Q 000087 1809 VINPGTLQSPQQSQSLSF-LAIDIYAKLMLSILKCCPVEQGSSKIFLLSKILTVTVKFILKDAEEKKASFNPRPYFRLFI 1887 (2284)
Q Consensus 1809 ~~~~g~~~~~~~~~~~~f-~~iDA~akLi~~lvk~~~~~~~~~k~~~L~kiL~iiv~vl~~dhe~~~~~FnqrpyfRlfs 1887 (2284)
.. ....+ .+++|+.+....|.+|.. +++|.+|++||+++|++|+++||+++|+.|||+||||+|+
T Consensus 1141 ~~-----------~a~~~i~tv~~~~~~l~~l~~f~d---~~tk~dl~~KI~~livgv~akdHs~~~e~f~~~~y~Rlf~ 1206 (1591)
T KOG1831|consen 1141 LI-----------TALVQICTVYAFICTLEMLDGFVD---LPTKIDLFNKILNLIVGVFAKDHSERGEYFNQCPYFRLFS 1206 (1591)
T ss_pred cc-----------ccchhhhhHHHHHHHHHHHHHHhc---CchHHHHHHHHHHHHHHHHhcchHHhhhhHhhCcHhHHHH
Confidence 21 12222 578888888888888852 2689999999999999999999999999999999999999
Q ss_pred HHHHhhcCCCCCCCcchHHHHHHHHHHhhhcCCCCCCchhhHHhHHhhcccchHHhhcCCCCCChHHHHHHHHHHHHhhh
Q 000087 1888 NWLLDMSSLDPVADGSNFQILSAFANAFHVLQPLKVPAFSFAWLELVSHRSFMPKLLIGNGQKGWPYIQRLLVNLLQFLE 1967 (2284)
Q Consensus 1888 ~LL~el~~~d~~l~~~~~~il~~fa~~l~~LqP~~~PgF~FaWl~LISHR~FmP~lL~~~~~~GW~~~~~LL~~ll~Fl~ 1967 (2284)
|+|.||..++.+++...++|+++|+++||.|||.++|||+||||+|||||+|+|++|..+++|||+.|++|+++|||||+
T Consensus 1207 ~ll~E~~~~~~~le~~~~~i~SaF~~tfhalqp~~~Pgf~fawL~lishr~li~~~L~~~~~k~~~~~~~llislfkfL~ 1286 (1591)
T KOG1831|consen 1207 MLLPELMTADSVLEPISLDILSAFKNTFHALQPRRFPGFAFAWLELISHRGLIPRMLAETNQKGWPLYAQLLISLFKFLA 1286 (1591)
T ss_pred HHHHHhccccchhhhHHHHHHHHHHHHHHHhCcccCcccceeeeecccchhHHHHHHHhccccccHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcCCCCCchHHHHhHhHHHHHHHHHhcchhHHHHHhHhhhccCCCCCccccceeecccCCCCCCCCCCCCCCCCCCCc
Q 000087 1968 PFLRNAELGVPVRFLYKGTLRVLLVLLHDFPEFLCDYHFTFCDVIPPSCIQMRNIILSAFPRNMRLPDPSTPNLKIDLLP 2047 (2284)
Q Consensus 1968 ~~L~~~~l~~~i~~lYkGtLRilLvLlHDfPEFL~~yh~~lc~~IP~~ciQLRNlILSA~P~~mrLPDPftp~Lkvd~Lp 2047 (2284)
||+||.+++++++.+|||||||+|||+||||||||+|||.|||.|||+|+||||+|||||||+|+|||||++|||||+||
T Consensus 1287 ~ylrn~~~~k~~~~lykgTLrVilvllhDfp~fl~~~hy~~~~~iPp~cvqlrniilsafp~~m~lpdpf~~~lkve~lp 1366 (1591)
T KOG1831|consen 1287 PYLRNYELFKPVQLLYKGTLRVILVLLHDFPEFLCEYHYGLCDTIPPNCVQLRNIILSAFPSNMRLPDPFAVNLKVEMLP 1366 (1591)
T ss_pred HHHhhhhhhhHHHHHHHcchHHhhcccccchHHHHHhhhhccCCCCcHHHHHHHHHHHhccccCcCCCccccccchhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcCCCCccccchHHHHHHhhhhHHHHHHhccCCCCccHHHHHHHHccCCccccccCCccccHhHHHHHHHHHHHHHHHhh
Q 000087 2048 EIRDPPRIFSEVDAALRAKQMRADVDDYLKTGQPGSSFLSELKQKLLLPPSEAASAGTRYNVPLINSLVLYVGMQAIHQL 2127 (2284)
Q Consensus 2048 Ei~~~P~i~~d~~~~L~~~~lk~~vD~yL~~r~~~~~~l~~l~~~L~~~~~~~~~~G~~yN~~liNAlVLyVG~~Ai~~~ 2127 (2284)
|+..+|+|+++++. +.+...|+++|.|+++|.+ .+|+..++.-++... .+|++||..+|||+|+|||++||.++
T Consensus 1367 e~~~ap~i~~~~~~-i~~~~~~~dl~a~l~s~~~-~t~l~~~~~~~~~~~----~~~~~~~~~~~naiVlyvG~~ai~~~ 1440 (1591)
T KOG1831|consen 1367 EGFYAPRILYSITQ-IMPSNFRKDLDARLKSSSP-VTFLSCLPQLLQVIK----EPGTRYNNQLINAIVLYVGIQAIAHL 1440 (1591)
T ss_pred hhhcCchhcCCHHH-hcccccCCCHHHHhhcccc-HhHHHHhhHHHHHhc----CccccccHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999 8888999999999999988 489999988777543 47999999999999999999999999
Q ss_pred hcccCCccccCCCCchhhhhhhhHHHHHHHHHhccChhhHHHHHHHHHhhhcCCChhhHHHHHHHHHHhhcccchhhHHH
Q 000087 2128 QTRTSHAQSTGNNSSLTAFLVSAALDIFQTLIQDLDTEGRYLFLNAAANQLRYPNNHTHYFSFVLLYLYAEANQEIIQEQ 2207 (2284)
Q Consensus 2128 ~~~~~~~~~~~~~~~~~~f~~s~~~~il~~L~~~ld~EgRY~ll~aiaNqLRYPN~HT~~FS~~lL~LF~~~~~~~IqEq 2207 (2284)
++++.+++++ +++|+++|+||++|+.+||+||||++++||||||||||+|||||||++||||.+++...||||
T Consensus 1441 ~~~~~~~~~~-------~it~s~~~~i~~nL~~nld~e~ry~~l~aianqlryp~~ht~~~s~~~l~lfk~~~~~pike~ 1513 (1591)
T KOG1831|consen 1441 RRKSQNPSTS-------TITHSAYMDIFQNLIVNLDTEGRYLLLNAIANQLRYPNSHTYYFSCVFLYLFKRAGNNPIKEQ 1513 (1591)
T ss_pred HhccCCCccc-------ccccCchhhHHHHHHHhcchhhhHHHHHHHHHHhcCCchhhHHHHHHHHHHHHhcCCCchHHH
Confidence 9988776554 467899999999999999999999999999999999999999999999999999988889999
Q ss_pred HHHHHHHHhccCCCCChHHHHHHHHHhhCCCCccccCCcCcchHHHHHHHHHHHHhcCCCCCCCc
Q 000087 2208 ITRVLFERLIVNRPHPWGLLITFIELIKNPRYNFWNQSFIRCAPEIEKLFESVARSCGGLKPVDD 2272 (2284)
Q Consensus 2208 ItRVLLERlIv~rPHPWGLliTFiELikNp~Y~Fw~~~Fv~~aPEIe~lF~svarsc~~~~~~~~ 2272 (2284)
|||+++||+||||||||||+|||+||||||.||||+||||+|||||.+||++|+++|+....+..
T Consensus 1514 i~~~~lerii~nrPHpWGllitF~eLikN~~YNfw~~~fv~~~pEI~rlfqsl~~~~~~~s~s~~ 1578 (1591)
T KOG1831|consen 1514 ITRVLLERIIVNRPHPWGLLITFTELIKNPDYNFWDHPFVQCAPEIKRLFQSLAKYCKAYSTSEQ 1578 (1591)
T ss_pred HHHHHHHHHhcCCCCCchhHHHHHHHHcCCCcccccCcccccCHHHHHHHHHHHHHhhCcccccc
Confidence 99999999999999999999999999999999999999999999999999999999997655544
No 3
>PF04054 Not1: CCR4-Not complex component, Not1; InterPro: IPR007196 The Ccr4-Not complex is a global regulator of gene expression that is conserved from yeast to human. It affects genes positively and negatively and is thought to regulate transcription factor IID function. In Saccharomyces cerevisiae, it exists in two prominent forms and consists of at least nine core subunits: the five Not proteins (Not1p to Not5p), Caf1p, Caf40p, Caf130p and Ccr4p []. The Ccr4-Not complex regulates many different cellular functions, including RNA degradation and transcription initiation. It may be a regulatory platform that senses nutrient levels and stress []. Caf1p and Ccr4p, are directly involved in mRNA deadenylation, and Caf1p is associated with Dhh1p, a putative RNA helicase thought to be a component of the decapping complex []. Pop2, a component of the Ccr4-Not complex, functions as a deadenylase []. The Ccr4-Not complex is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID [].
Probab=100.00 E-value=2.4e-115 Score=1066.24 Aligned_cols=366 Identities=59% Similarity=1.058 Sum_probs=343.3
Q ss_pred HHHHhhcCCCC--CCCcch--HHHHHHHHHHhhhcCCCCCCchhhHHhHHhhcccchHHhhc-CCCCCChHHHHHHHHHH
Q 000087 1888 NWLLDMSSLDP--VADGSN--FQILSAFANAFHVLQPLKVPAFSFAWLELVSHRSFMPKLLI-GNGQKGWPYIQRLLVNL 1962 (2284)
Q Consensus 1888 ~LL~el~~~d~--~l~~~~--~~il~~fa~~l~~LqP~~~PgF~FaWl~LISHR~FmP~lL~-~~~~~GW~~~~~LL~~l 1962 (2284)
||||||+..+. .++..+ .+++.+||++||.|||.++|||+|||++|||||+|||+||. .++++||+.|++||+++
T Consensus 1 ~ll~e~~~~~~~~~~~~~~~~~~~~~~fa~~l~~lqP~~~PgF~faWl~LisHR~Flp~lL~~~~~~~gW~~~~~Ll~~l 80 (379)
T PF04054_consen 1 SLLCELHAISIEDSLESEELDRQFLLAFASFLHSLQPLYFPGFAFAWLELISHRMFLPKLLRNSPDQKGWPAYTRLLIDL 80 (379)
T ss_pred CeeeecccCcccccchhhhhHHHHHHHHHHHHHhcCCccCcchHHHHHHHHHHHHHHHHHHhcCCCCCChHHHHHHHHHH
Confidence 58999995332 334334 59999999999999999999999999999999999999999 88999999999999999
Q ss_pred HHhhhhhhcCCCCCchHHHHhHhHHHHHHHHHhcchhHHHHHhHhhhccCCCCCccccceeecccCCCCCCCCCCCCCCC
Q 000087 1963 LQFLEPFLRNAELGVPVRFLYKGTLRVLLVLLHDFPEFLCDYHFTFCDVIPPSCIQMRNIILSAFPRNMRLPDPSTPNLK 2042 (2284)
Q Consensus 1963 l~Fl~~~L~~~~l~~~i~~lYkGtLRilLvLlHDfPEFL~~yh~~lc~~IP~~ciQLRNlILSA~P~~mrLPDPftp~Lk 2042 (2284)
|+|+++|+|+.+++++++++||||||++|||+||||||||+||++||++||+||+||||+||||||++|+|||||+||+|
T Consensus 81 l~Fl~~~l~~~~~~~~~~~lYkg~LRillvL~HDfPeFL~~~h~~lc~~iP~~ciQLrNiILsA~P~~~~lpDPf~~~lk 160 (379)
T PF04054_consen 81 LKFLGPYLKNEELSDAIKVLYKGTLRILLVLLHDFPEFLCEYHFSLCDVIPPHCIQLRNIILSAFPRNMKLPDPFTPGLK 160 (379)
T ss_pred HHHHHHhccccccchHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHhcChhHHHHHHHHHHhCCCCCCCCCCCCCCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCcCcCCCCccccchHHHHHHhhhhHHHHHHhccCCCCccHHHHHHHHccCCcccccc----CCccccHhHHHHHHHH
Q 000087 2043 IDLLPEIRDPPRIFSEVDAALRAKQMRADVDDYLKTGQPGSSFLSELKQKLLLPPSEAAS----AGTRYNVPLINSLVLY 2118 (2284)
Q Consensus 2043 vd~LpEi~~~P~i~~d~~~~L~~~~lk~~vD~yL~~r~~~~~~l~~l~~~L~~~~~~~~~----~G~~yN~~liNAlVLy 2118 (2284)
||++|||+++|.|++|++..|++.+||+.||+||++| ++++++++|+++|+.++.+... .|++||+++|||+|+|
T Consensus 161 vd~l~e~~~~P~i~~d~~~~L~~~~lk~~vd~~l~~~-~~~~~l~~i~~~l~~~~~~~~~~~g~~~~~~n~~linalVly 239 (379)
T PF04054_consen 161 VDRLPEIKQAPKILSDPTEDLQQAGLKKPVDQYLRNG-PSESLLAQILHKLQLPEPEETNGFGFDGVKYNVKLINALVLY 239 (379)
T ss_pred chhchhhccCCccccchhhhcchHHHHHHHHHHHHhC-CCHHHHHHHHHHhcCCccccccccCCCCccccHHHHHHHHHH
Confidence 9999999999999999999999999999999999874 4579999999999998876543 5699999999999999
Q ss_pred HHHHHHHhhhcccCCccccCCCCchhhhhhhhHHHHHHHHHhccChhhHHHHHHHHHhhhcCCChhhHHHHHHHHHHhh-
Q 000087 2119 VGMQAIHQLQTRTSHAQSTGNNSSLTAFLVSAALDIFQTLIQDLDTEGRYLFLNAAANQLRYPNNHTHYFSFVLLYLYA- 2197 (2284)
Q Consensus 2119 VG~~Ai~~~~~~~~~~~~~~~~~~~~~f~~s~~~~il~~L~~~ld~EgRY~ll~aiaNqLRYPN~HT~~FS~~lL~LF~- 2197 (2284)
||++|+.+.++++..+.+.++ ++++++|++|++++|+||||++++||||||||||+|||||||+||+||+
T Consensus 240 vg~~a~~~~~~~~~~~~f~~~---------s~~~~ll~~Li~~ld~E~RY~ll~aiaNqLRYPN~HT~~Fs~~lL~lF~~ 310 (379)
T PF04054_consen 240 VGIQAVAEAQKKSSAPSFNTK---------SPHVTLLSKLIHELDPEGRYYLLSAIANQLRYPNSHTHFFSCVLLNLFSS 310 (379)
T ss_pred HhHHHHHHHhccCCCcccccc---------ChHHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCchhHHHHHHHHHHHhcC
Confidence 999999887776665555543 6899999999999999999999999999999999999999999999999
Q ss_pred ---cccchhhHHHHHHHHHHHhccCCCCChHHHHHHHHHhhCCCCccccCCcCcchHHHHHHHHHHHHh
Q 000087 2198 ---EANQEIIQEQITRVLFERLIVNRPHPWGLLITFIELIKNPRYNFWNQSFIRCAPEIEKLFESVARS 2263 (2284)
Q Consensus 2198 ---~~~~~~IqEqItRVLLERlIv~rPHPWGLliTFiELikNp~Y~Fw~~~Fv~~aPEIe~lF~svars 2263 (2284)
+.++++||||||||||||+||+|||||||+|||+||+|||+|+||++|||||+||||++|++|+||
T Consensus 311 ~~~~~~~~~IqEqItRVLLERliv~rPHPWGllitfiELikN~~y~f~~~pFik~~pEI~~~f~~~~~~ 379 (379)
T PF04054_consen 311 DMNDPNDEDIQEQITRVLLERLIVNRPHPWGLLITFIELIKNPKYNFWELPFIKCAPEIEKLFESLARH 379 (379)
T ss_pred CCCccchhhhHHHHHHHHHHHHhcCCCCCccHHHHHHHHHhCccCCcccCcccccCHHHHHHHHHHhcC
Confidence 667899999999999999999999999999999999999999999999999999999999999986
No 4
>PF12842 DUF3819: Domain of unknown function (DUF3819); InterPro: IPR024557 The Ccr4-Not complex is a global regulator of gene expression that is conserved from yeast to human. It affects genes positively and negatively and is thought to regulate transcription factor IID function. In Saccharomyces cerevisiae, it exists in two prominent forms and consists of at least nine core subunits: the five Not proteins (Not1p to Not5p), Caf1p, Caf40p, Caf130p and Ccr4p []. The Ccr4-Not complex regulates many different cellular functions, including RNA degradation and transcription initiation. It may be a regulatory platform that senses nutrient levels and stress []. Caf1p and Ccr4p, are directly involved in mRNA deadenylation, and Caf1p is associated with Dhh1p, a putative RNA helicase thought to be a component of the decapping complex []. Pop2, a component of the Ccr4-Not complex, functions as a deadenylase []. This entry represents a domain of unknown function found in the Not1 subunit of the CCR4-Not complex.
Probab=100.00 E-value=2.5e-46 Score=405.04 Aligned_cols=145 Identities=56% Similarity=0.809 Sum_probs=140.2
Q ss_pred chhhhhhHHHHHHHHHHhhhhhcchhhHHHHHHHHHHHHhhccCCChhhHHHHHHHHHHHHHHHhhhhHHHchHHHHHHH
Q 000087 1171 HLHFQRVVPIAMDRAIKEIVSGIVQRSVSIATQTTKELVLKDYAMESDETRIYNAAHLMVASLAGSLAHVTCKEPLRGSI 1250 (2284)
Q Consensus 1171 ~p~Lk~iV~~AidRAIrEII~PVVeRSVtIA~iTT~eLV~KDFA~E~DE~kmr~AAh~MVr~LAgSLAlVTckEPLr~si 1250 (2284)
||+||++|+.|+||||||||.|||||||+||++||++||+||||+||||+|||+|||+||++||||||+|||||||+.+|
T Consensus 1 ~p~lk~~v~~Al~rai~Eii~pvveRsv~IA~~Tt~~LV~KDFa~E~De~~~r~aa~~Mv~~LA~sLalvTcrepL~~~i 80 (147)
T PF12842_consen 1 HPQLKRIVQNALDRAIREIISPVVERSVTIASITTEELVKKDFATEPDENKMRRAAHNMVRSLAGSLALVTCREPLRESI 80 (147)
T ss_pred ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcC-CC-cHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 000087 1251 SSQLRNSLQGL-TI-ASELLEQAVQLVTNDNLDLGCAVIEQAATDKAIQTIDGEIAQQLSLRRKHRE 1315 (2284)
Q Consensus 1251 ~~~Lr~~l~~~-~~-~~~~~Eq~i~~~vnDNldLac~iIEKaA~EKAi~eIDe~l~~~~~~RRkhre 1315 (2284)
.+|||+++++. +. .++++|++++++++||+||||++|||+|+|||++|||++|+++|+.||+|||
T Consensus 81 ~~~l~~~l~~~~~~~~~~~~e~~i~~~~~dNlel~~~~Iek~a~eka~~~id~~l~~~~~~R~~~re 147 (147)
T PF12842_consen 81 QNNLRSLLSQLNGSTEQELPEQAIQQIVNDNLELACAFIEKAAMEKAIKEIDERLEPEIELRRRHRE 147 (147)
T ss_pred HHHHHHHHHhhcCCchhhhHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 99999999843 33 4689999999999999999999999999999999999999999999999996
No 5
>KOG1831 consensus Negative regulator of transcription [Transcription]
Probab=97.54 E-value=0.11 Score=72.01 Aligned_cols=294 Identities=22% Similarity=0.260 Sum_probs=182.1
Q ss_pred HHhhcccCCchhHHHHHHHHHhCChhHHHHHHHHHHH-HHHHHhcccccccChHHHHHHHhhhhhHhhhhhhcCcccccC
Q 000087 873 VMKRASIEPNFHDLYLKFLDKVNSKALNREIVQATYE-NCKVLLGSELIKSSSEERSLLKNLGSWLGKLTIGRNQVLRAR 951 (2284)
Q Consensus 873 V~kRAsiEPNfH~LYl~fl~~l~~~~L~~~Vl~~Ty~-~i~~LL~se~~~~ss~eRslLKNLGsWLG~iTLarNkPI~~k 951 (2284)
+.|==..|++=..||+.+... .+.|-+-+...|.+ -+++..++.. -+...=+=.+..|.++-+..-
T Consensus 658 irKDFA~e~~es~l~~Aa~~M--~r~la~~lAmiTcreplk~am~~nl-----------~~~~~~~l~~~~ai~~a~~t~ 724 (1591)
T KOG1831|consen 658 IRKDFALERDESRLRLAASQM--VRELAAGLAMITCREPLKVAMSSNL-----------VLAALSLLSLMAAIARAADTL 724 (1591)
T ss_pred HHHHHhcccchhHHHHHHHHH--HHHHHHHHHHHhhhhHHHHHHHhhH-----------HHHHhhhhHHHHHHHHHHHHH
Confidence 344445788888888887655 34455555555554 2333333221 111111111577888888888
Q ss_pred CCChhHHHHHHHhcCceEEEechhhhhccccCCCccccCCCccHHHHHHHHHHHhcCCcccchhHHHHHHHHhhcCCCcc
Q 000087 952 EIDPKSLIIEAYEKGLMIAVIPFTSKILEPCQSSLAYQPPNPWTMAILGLLAEIYSMPNLKMNLKFDIEVLFKNLGVDMK 1031 (2284)
Q Consensus 952 ~ld~K~LL~eaY~~g~L~~VIPFV~KVLe~~~~S~vFkPPNPWtm~IL~lL~Ely~~~~LKlnLKFEIEVL~K~L~ld~~ 1031 (2284)
--|.+.+.+.-.++-++.-.+-++.+-|++...-+||.+.|||.|.++-.+.+.|++- |- +-++++..
T Consensus 725 ~~dNv~l~~~~Iek~a~eka~~dI~~~L~q~~~~Rv~~k~~~~~~~fvD~~~~~~~~~-LP-----------~~vr~~~~ 792 (1591)
T KOG1831|consen 725 QSDNVELVVKFIEKTAIEKATQDIDSRLEQDICGRVFHKENPEVMPFVDLLSAAYSCT-LP-----------EVVRLKIG 792 (1591)
T ss_pred HhhchhhHhhhhHHHHHHHHHHHHHHHHHHhhHhheecccCCccccchhhhhhhhhcc-Cc-----------HhhhcccC
Confidence 8889999999999999999999999999999999999999999999999999999875 22 22223222
Q ss_pred ccccccccccchhhccCCCCCCCCCcCCCCCcccCCCCcCccCCCCCCCCCCCcCCCCCCCCCcccccccccccccCcCc
Q 000087 1032 DITPTSLLKDRKREIEGNPDFSNKDVGASQPQLVPEVKPAIVSPLGHVDLPLDVASPPNSGGPTHLLSQYAAPLRLSSGT 1111 (2284)
Q Consensus 1032 dieps~~L~~r~~~~~~~~d~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~q~~~~~~~~~~~ 1111 (2284)
.+.|.-+ +-.++ |.. ..+ +++
T Consensus 793 ~~~~~l~-----~vYe~---F~k---------~i~-----------------------------~~~------------- 813 (1591)
T KOG1831|consen 793 GLTPQLF-----RVYEE---FPK---------PIP-----------------------------GFL------------- 813 (1591)
T ss_pred CCCHHHH-----HHHHH---ccc---------ccc-----------------------------ccc-------------
Confidence 2222211 00000 000 000 000
Q ss_pred chhHHHHhhccCCCCCCcccccccccCCCCCCCccccccCCCCCCccEeecccccccccchhhhhhHHHHHHHHHHhhhh
Q 000087 1112 LMEDEKLAALGISDQLPSAQGLFQASQSQSPFSVSQLSTPIPNIGTHVIINQKLTALGLHLHFQRVVPIAMDRAIKEIVS 1191 (2284)
Q Consensus 1112 l~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~s~~~i~~~ip~l~~~~~i~~~l~~~~~~p~Lk~iV~~AidRAIrEII~ 1191 (2284)
|+ ...+++..++.=+..+ + -...+..+.+-..+||.+
T Consensus 814 ----------~~--------------------------s~~~~la~~~~~~~dl---t----~~~~~s~~~~lv~~ei~~ 850 (1591)
T KOG1831|consen 814 ----------GN--------------------------SSRKDLAEYITESSDL---T----QPHVISNALDLVVREICG 850 (1591)
T ss_pred ----------cc--------------------------CCCcccccccCCCccc---c----chhhhhHHHHHHHHHHHH
Confidence 00 0000011110001000 0 013458899999999999
Q ss_pred hcchhhHHHHHHHHHHHHhhccCCChhhHHHHHHHHHHHHHHHhhhhHHHchHHHHHHHHHHHHHHhhcCCCcHHHHHHH
Q 000087 1192 GIVQRSVSIATQTTKELVLKDYAMESDETRIYNAAHLMVASLAGSLAHVTCKEPLRGSISSQLRNSLQGLTIASELLEQA 1271 (2284)
Q Consensus 1192 PVVeRSVtIA~iTT~eLV~KDFA~E~DE~kmr~AAh~MVr~LAgSLAlVTckEPLr~si~~~Lr~~l~~~~~~~~~~Eq~ 1271 (2284)
-.++|+...|..+.+ +-.|-+.+++--+.+ =|.+|+-+++.|+..+.. +++..-|..|.-....++. ..---+-
T Consensus 851 ~~~~~a~~~~i~~~~-l~~~a~s~~~~m~~v--~~~~~~~~~~~~~~~~~a-r~i~hli~~~V~~~~~~l~--~~~~~~~ 924 (1591)
T KOG1831|consen 851 AIVEKACQTAIQTGM-LQFKAQSVEKLMEEV--PARNMVVNLVNSLLLLVA-RSIEHLISGLVSYFMKNLE--LDFSTEK 924 (1591)
T ss_pred HHHHHHHHHHHHhhh-hhhhhhcchhhHHhc--cchhhhHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHH--Hhhcchh
Confidence 999998888887777 778888887765555 577999999999988777 6666666555443222111 1111123
Q ss_pred HHHHHHhhHHHHHHHHHHHHHHHHHHHH
Q 000087 1272 VQLVTNDNLDLGCAVIEQAATDKAIQTI 1299 (2284)
Q Consensus 1272 i~~~vnDNldLac~iIEKaA~EKAi~eI 1299 (2284)
|..++-.|++.+|.+++|++..|...-|
T Consensus 925 I~~i~m~iL~~ic~~~qk~~~~~vs~a~ 952 (1591)
T KOG1831|consen 925 IFKIIMEILDNICRFIQKAGVRKVSEAI 952 (1591)
T ss_pred HHHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence 5678889999999999999988554433
No 6
>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=91.47 E-value=1.5 Score=50.44 Aligned_cols=181 Identities=20% Similarity=0.249 Sum_probs=120.0
Q ss_pred HhHhhhhhcCCcccHHHHHHHHHHHhhhc--chhhhhHHHHHhhcccCCchhHHHHHHHHHhCC--hhHHHHHHHHHHHH
Q 000087 835 DKISFIINNISALNVEAKAKEFTEILKEQ--YYPWFAQYMVMKRASIEPNFHDLYLKFLDKVNS--KALNREIVQATYEN 910 (2284)
Q Consensus 835 DKI~FIiNNlS~~Nle~K~~Elke~L~~~--y~~WFA~YLV~kRAsiEPNfH~LYl~fl~~l~~--~~L~~~Vl~~Ty~~ 910 (2284)
.+|.-++|-+|++|++.-++|+.+..... ...-+... +.+++-.+|+|-.+|..++..++. +.+-..+++.++..
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 46778999999999999999999888653 33333333 457799999999999999999987 46777788888777
Q ss_pred HHHHhcccccccChHHHHHHHhhhhhHhhhhhhcCcccccCCCChhHHHHHHHhcCce------EEEechhhhhccccCC
Q 000087 911 CKVLLGSELIKSSSEERSLLKNLGSWLGKLTIGRNQVLRAREIDPKSLIIEAYEKGLM------IAVIPFTSKILEPCQS 984 (2284)
Q Consensus 911 i~~LL~se~~~~ss~eRslLKNLGsWLG~iTLarNkPI~~k~ld~K~LL~eaY~~g~L------~~VIPFV~KVLe~~~~ 984 (2284)
....+... ...++...+|+--+||.+..-+=-+.. .+.+++-+--....- ..-|=.+|.+|+.|..
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 76654432 335667778888888888765443322 122222222222211 1344567788888866
Q ss_pred CccccCCCccHHH-HHHHHHHHhcCC---cccchhHHHHHHHHhh
Q 000087 985 SLAYQPPNPWTMA-ILGLLAEIYSMP---NLKMNLKFDIEVLFKN 1025 (2284)
Q Consensus 985 S~vFkPPNPWtm~-IL~lL~Ely~~~---~LKlnLKFEIEVL~K~ 1025 (2284)
.--+ +.+|=.|. ++..+....... ++....+|-+|-|+.-
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 5433 56665554 445555555555 5777788888877653
No 7
>KOG1467 consensus Translation initiation factor 2B, delta subunit (eIF-2Bdelta/GCD2) [Translation, ribosomal structure and biogenesis]
Probab=83.80 E-value=3.3 Score=53.24 Aligned_cols=127 Identities=22% Similarity=0.280 Sum_probs=91.8
Q ss_pred HHHHHHHhhhhhcchhhHHHHHHHHHHHHhhccCCChhhHHHHHHHHHHHHHHHhhhhHHHchHHHHHHHHHHHHHHhhc
Q 000087 1181 AMDRAIKEIVSGIVQRSVSIATQTTKELVLKDYAMESDETRIYNAAHLMVASLAGSLAHVTCKEPLRGSISSQLRNSLQG 1260 (2284)
Q Consensus 1181 AidRAIrEII~PVVeRSVtIA~iTT~eLV~KDFA~E~DE~kmr~AAh~MVr~LAgSLAlVTckEPLr~si~~~Lr~~l~~ 1260 (2284)
.+.-|-.. |.-.--| -||.+-+-+.|.|||-+++.. .-.|.|...+.+=+++.|---||-.||.|-+|-+=+.
T Consensus 241 glq~a~~k-I~GsnaR--CIa~L~afqevi~Dy~TP~~k----tlsrdLt~~i~~qv~~L~~cRPLs~SmgNAiRflK~e 313 (556)
T KOG1467|consen 241 GLQYALGK-ISGSNAR--CIAMLQAFQEVIKDYTTPPEK----TLSRDLTAAISPQVSFLTQCRPLSISMGNAIRFLKNE 313 (556)
T ss_pred HHHHhhcc-cCCccHH--HHHHHHHHHHHHHhccCCCcc----ccchhhHhhhhhHHHHHhhcCCccchhhHHHHHHHHH
Confidence 33333333 4444444 499999999999999999987 4678888888888887776689999999999976322
Q ss_pred ---CC---C---cHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHhh
Q 000087 1261 ---LT---I---ASELLEQAVQLVTNDNLDLGCAVIEQAATDKAI-----------QTIDGEIAQQLSLRRKHR 1314 (2284)
Q Consensus 1261 ---~~---~---~~~~~Eq~i~~~vnDNldLac~iIEKaA~EKAi-----------~eIDe~l~~~~~~RRkhr 1314 (2284)
+. + .++.+-..|..-+++++.+|-..|-+.|.+|.- .-++..|..+-+.+++.|
T Consensus 314 I~~L~~s~~e~eaKe~L~~~I~~~i~eki~~A~qaI~q~a~~KI~dgdviltyg~s~vV~~ill~A~~~~k~fr 387 (556)
T KOG1467|consen 314 ISKLPISLSESEAKEELQSDIDRFIAEKIILADQAISQHAVTKIQDGDVLLTYGSSSVVNMILLEAKELGKKFR 387 (556)
T ss_pred HhhCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEecchHHHHHHHHHHHHhCcceE
Confidence 22 1 245566678889999999999999999999842 234445666665444444
No 8
>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=79.18 E-value=5.6 Score=45.67 Aligned_cols=108 Identities=19% Similarity=0.254 Sum_probs=79.1
Q ss_pred hHhhhhhcCCcccHHHHHHHHHHHhhhcchhhhhHHH---HHhhcccCCchhHHHHHHHHHhCCh---hHHHHHHHHHHH
Q 000087 836 KISFIINNISALNVEAKAKEFTEILKEQYYPWFAQYM---VMKRASIEPNFHDLYLKFLDKVNSK---ALNREIVQATYE 909 (2284)
Q Consensus 836 KI~FIiNNlS~~Nle~K~~Elke~L~~~y~~WFA~YL---V~kRAsiEPNfH~LYl~fl~~l~~~---~L~~~Vl~~Ty~ 909 (2284)
||.-++|-+|..|++.-++++.+..... .++...++ +.++|..+|+|..+|..++..+... .+-..+++.+..
T Consensus 3 ~v~~~lnklt~~n~~~~~~~l~~~~~~~-~~~~~~~i~~~i~~~a~~~~~~~~~~a~l~~~l~~~~~~~f~~~ll~~~~~ 81 (209)
T PF02854_consen 3 KVRGILNKLTPSNFESIIDELIKLNWSD-DPETLKEIVKLIFEKAVEEPNFSPLYARLCAALNSRFPSEFRSLLLNRCQE 81 (209)
T ss_dssp HHHHHHHHCSSTTHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHSGGGHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred hHHHHHHHCCHHHHHHHHHHHHHHHhhc-cHHHHHHHHHHHhhhhhcCchHHHHHHHHHHHHhccchhhHHHHHHHHHHH
Confidence 6778999999999999999999998776 33443333 3567999999999999999998743 455666666665
Q ss_pred HHHHHh-cccccccChHHHHHHHhhhhhHhhhhhhc
Q 000087 910 NCKVLL-GSELIKSSSEERSLLKNLGSWLGKLTIGR 944 (2284)
Q Consensus 910 ~i~~LL-~se~~~~ss~eRslLKNLGsWLG~iTLar 944 (2284)
.+.... ..+.......++...+|+.-+||.+....
T Consensus 82 ~f~~~~~~~~~~~~~~~~~~~~~~~~~fl~eL~~~~ 117 (209)
T PF02854_consen 82 EFEERYSNEELEENRQSSKQRRRGNIRFLAELFNFG 117 (209)
T ss_dssp HHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred HHHHhhhhhhHHHHHHHHHHHHhhhhhHHHhhHhhc
Confidence 554411 01222345677888899999999887654
No 9
>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=42.29 E-value=1.7e+02 Score=30.83 Aligned_cols=71 Identities=15% Similarity=0.322 Sum_probs=56.0
Q ss_pred CHHHHHHHHHHhhcCCcccchhhHHhHHHhhhhhhccCCCCcHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHHhcC
Q 000087 549 TIEAMVQMLARFKESSVKREHSIFECMIGNLFEEYRFFPKYPERQLRIAAVLFGSIIKHQLVTHLTLGIALRGVLDALRK 628 (2284)
Q Consensus 549 sI~~iv~~L~r~K~S~~~rdqdiFaCMIh~LFdEYrFf~~YP~~eL~iTAvLFG~lI~~~Lv~~~~L~iALr~ILeAlrk 628 (2284)
..+|.+..+++++-+ ....++..-+|+..+|+ =..+-..++.|+..+++.++++...+.-|+.-+++.+.+
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 678888888887666 56678888888888988 355566699999999999999999999988888877654
No 10
>COG5088 SOH1 Rad5p-binding protein [General function prediction only]
Probab=36.88 E-value=73 Score=33.35 Aligned_cols=89 Identities=24% Similarity=0.339 Sum_probs=65.9
Q ss_pred ccHHHHHHHHHHHhhhcchhhhhHHHHHhhcccCCchhHHHHHHHHHhCChhHHHHHHHHHHHHHHHHhcccccccChHH
Q 000087 847 LNVEAKAKEFTEILKEQYYPWFAQYMVMKRASIEPNFHDLYLKFLDKVNSKALNREIVQATYENCKVLLGSELIKSSSEE 926 (2284)
Q Consensus 847 ~Nle~K~~Elke~L~~~y~~WFA~YLV~kRAsiEPNfH~LYl~fl~~l~~~~L~~~Vl~~Ty~~i~~LL~se~~~~ss~e 926 (2284)
+-+|-.++=+.-+-.+.|..|+++.=.-+ -+|| .-|++.++--.+|+-.++|+--+.--|-.||++......-+|
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----SENF-KNYLKYLEYWRNPEYSQFIVYPNCLFILKLLNGFMESAIVSE 89 (114)
T ss_pred chhHHHHHHHHHhcCHHHHHHHHHhhhhc----CHHH-HHHHHHHHHhhCCcccceeechhHHHHHHHhcchhHhhhhhh
Confidence 34444444344444678888887754443 3444 569999999999999899887777778888998887777889
Q ss_pred HHHHHhhh-----hhHhhh
Q 000087 927 RSLLKNLG-----SWLGKL 940 (2284)
Q Consensus 927 RslLKNLG-----sWLG~i 940 (2284)
-.++|.|| -|||+.
T Consensus 90 ~~l~~~l~e~qy~~Wlnk~ 108 (114)
T COG5088 90 DGLLEGLDELQYPQWLNKM 108 (114)
T ss_pred hHHHHhhhHHHHHHHHHHH
Confidence 99999998 488765
No 11
>cd00686 Terpene_cyclase_cis_trans_C1 Cis, Trans, Terpene Cyclases, Class 1. This CD includes the terpenoid cyclase, trichodiene synthase, which catalyzes the cyclization of farnesyl diphosphate (FPP) to trichodiene using a cis-trans pathway, and is the first committed step in the biosynthesis of trichothecene toxins and antibiotics. As with other enzymes with the 'terpenoid synthase fold', this enzyme has two conserved metal binding motifs that coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function as homodimers and are found in several genera of fungi.
Probab=28.07 E-value=95 Score=39.45 Aligned_cols=73 Identities=25% Similarity=0.461 Sum_probs=46.5
Q ss_pred chHHhhcCCCCC--ChHHHHHHHHHHHHhhhhhhcCCCCCchHHHHhHhHHHHHHHHH------------hcchhHHHHH
Q 000087 1939 FMPKLLIGNGQK--GWPYIQRLLVNLLQFLEPFLRNAELGVPVRFLYKGTLRVLLVLL------------HDFPEFLCDY 2004 (2284)
Q Consensus 1939 FmP~lL~~~~~~--GW~~~~~LL~~ll~Fl~~~L~~~~l~~~i~~lYkGtLRilLvLl------------HDfPEFL~~y 2004 (2284)
|--.|+....|+ -|..+..+|-+++++.+||-- ..++|+||..+-... +|||+||-.
T Consensus 113 f~~dL~~G~~qkhP~l~~v~~~l~~~lr~fGpF~s--------~~IikSTLdFv~g~~iEq~nf~~~p~A~~fP~ylR~- 183 (357)
T cd00686 113 YFDDLQAGREQAHPWWALVNEHFPNVLRHFGPFCS--------LNLIRSTLDFFEGCWIEQYNFGGFPGSHDYPQFLRR- 183 (357)
T ss_pred HHHHHhcCCCCCCcHHHHHHHHHHHHHHHhhhhhH--------HHHHHHHHHHHHHHHHhhhccCCCCCCcccchHHHh-
Confidence 333444433333 377777888888888888865 568899998865442 478888743
Q ss_pred hHhhhccCCCCCccccceeecccCCC
Q 000087 2005 HFTFCDVIPPSCIQMRNIILSAFPRN 2030 (2284)
Q Consensus 2005 h~~lc~~IP~~ciQLRNlILSA~P~~ 2030 (2284)
-+-++.- .-.+.||+.
T Consensus 184 ----ksGl~E~------yA~FiFPk~ 199 (357)
T cd00686 184 ----MNGLGHC------VGASLWPKE 199 (357)
T ss_pred ----ccCCcce------eEEEecchh
Confidence 3334332 356778875
No 12
>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=24.43 E-value=3.6e+02 Score=28.49 Aligned_cols=71 Identities=13% Similarity=0.279 Sum_probs=60.3
Q ss_pred CHHHHHHHHHHhhcCCcccchhhHHhHHHhhhhhhccCCCCcHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHHhcC
Q 000087 549 TIEAMVQMLARFKESSVKREHSIFECMIGNLFEEYRFFPKYPERQLRIAAVLFGSIIKHQLVTHLTLGIALRGVLDALRK 628 (2284)
Q Consensus 549 sI~~iv~~L~r~K~S~~~rdqdiFaCMIh~LFdEYrFf~~YP~~eL~iTAvLFG~lI~~~Lv~~~~L~iALr~ILeAlrk 628 (2284)
..+|.+..+++++-+ ....++....|+--+||= .++-..++.|+..+.+.++++...+.-|+.-+++.+.+
T Consensus 17 D~~ea~~~l~~L~~~--~~~~~vv~~~i~~~le~~-------~~~~~~~~~Ll~~L~~~~~~~~~~~~~~f~~~~~~l~d 87 (113)
T smart00544 17 DTDEAVHCLLELKLP--EQHHEVVKVLLTCALEEK-------RTYREMYSVLLSRLCQANVISTKQFEKGFWRLLEDIED 87 (113)
T ss_pred CHHHHHHHHHHhCCC--cchHHHHHHHHHHHHcCC-------ccHHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhhChh
Confidence 678888888888766 377899999999999982 34566699999999999999999999999999988876
No 13
>PRK00218 putative lysogenization regulator; Reviewed
Probab=20.55 E-value=2.1e+02 Score=34.25 Aligned_cols=90 Identities=20% Similarity=0.368 Sum_probs=60.5
Q ss_pred chhhHHhHHHhhhhhhccCCCCcHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHHhc---CCCCCc--ccchHHHHH
Q 000087 568 EHSIFECMIGNLFEEYRFFPKYPERQLRIAAVLFGSIIKHQLVTHLTLGIALRGVLDALR---KPADSK--MFVFGTKAL 642 (2284)
Q Consensus 568 dqdiFaCMIh~LFdEYrFf~~YP~~eL~iTAvLFG~lI~~~Lv~~~~L~iALr~ILeAlr---kp~~Sk--Mf~FGiqAL 642 (2284)
|.+-|.|+|++||.- +| ..|..+||+ +. .|..||+.+.+.|. ++.+.. -|.+|+.+|
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 567899999999974 34 458889998 22 27888888888886 343333 366777777
Q ss_pred HHHHHhhhhhhHHHHHHhc--------ccccccccHHHHHHHHH
Q 000087 643 EQFVDRLIEWPQYCNHILQ--------ISHLRSTHAELVAFIER 678 (2284)
Q Consensus 643 ~qF~~RL~EwPqyC~~Ll~--------ip~L~~~~p~l~~~ie~ 678 (2284)
|+ ||..=|..-..|.+ ..||.-+|+.++..+-.
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 65 55556666555532 35676678877765433
Done!