Query 000444
Match_columns 1498
No_of_seqs 155 out of 270
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 08:57:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000444.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000444hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1831 Negative regulator of 100.0 6E-244 1E-248 2213.2 77.9 1192 38-1486 370-1578(1591)
2 COG5103 CDC39 Cell division co 100.0 1E-228 2E-233 2031.7 67.4 1199 40-1485 781-1991(2005)
3 PF04054 Not1: CCR4-Not comple 100.0 2E-115 5E-120 1026.7 30.5 366 1102-1477 1-379 (379)
4 PF12842 DUF3819: Domain of un 100.0 3.8E-47 8.3E-52 395.3 17.7 145 385-529 1-147 (147)
5 KOG1831 Negative regulator of 97.7 0.047 1E-06 72.7 34.1 240 154-513 713-952 (1591)
6 smart00543 MIF4G Middle domain 94.6 0.39 8.5E-06 52.4 12.5 179 49-238 2-195 (200)
7 PF02854 MIF4G: MIF4G domain; 92.0 0.17 3.6E-06 55.3 4.4 188 50-238 3-204 (209)
8 KOG1467 Translation initiation 83.8 3.6 7.7E-05 50.9 8.5 112 413-528 256-387 (556)
9 COG5088 SOH1 Rad5p-binding pro 35.8 87 0.0019 31.4 5.7 89 61-154 15-108 (114)
10 cd00686 Terpene_cyclase_cis_tr 31.2 80 0.0017 38.4 5.6 61 1165-1244 127-199 (357)
11 KOG3091 Nuclear pore complex, 22.6 9.6E+02 0.021 30.8 12.7 27 424-450 404-430 (508)
12 cd05133 RasGAP_IQGAP1 IQGAP1 i 21.5 9.9E+02 0.021 29.6 12.7 42 398-449 54-95 (360)
13 KOG2051 Nonsense-mediated mRNA 21.4 2.4E+03 0.053 29.9 18.9 96 771-867 461-569 (1128)
No 1
>KOG1831 consensus Negative regulator of transcription [Transcription]
Probab=100.00 E-value=6.4e-244 Score=2213.25 Aligned_cols=1192 Identities=39% Similarity=0.622 Sum_probs=959.4
Q ss_pred CCCCCCCHHhhhhhhhhcccCChhhHHHHHHHHHHHhhhcChhHHHHHHHhhhcccCcchhHHHHHHHHHhCChhHHHHH
Q 000444 38 TPIEAPASEVQDKISFIINNISALNVEAKAKEFTEILKEQYYPWFAQYMVMKRASIEPNFHDLYLKFLDKVNSKALNREI 117 (1498)
Q Consensus 38 ~~~e~P~e~v~dki~Fi~NNls~~Nl~~K~~El~~~l~~~y~~WFa~YLV~~Ras~EpN~H~lY~~~l~~l~~~~L~~~i 117 (1498)
++-+.|||+|+|||+|++||+|+.|+.+|++|+|++|+|+||+|||+|||.||||+|+|||+||.+|+++|++.
T Consensus 370 ~n~~~~~e~v~dkilF~lNNlsq~N~~qKvdevk~~ltp~y~~Wfs~YiV~qR~S~E~Nf~~LYskFi~ai~n~------ 443 (1591)
T KOG1831|consen 370 KNAEGPPEDVVDKILFPLNNLSQLNFNQKVDEVKEILTPEYYPWFSQYIVTQRVSKEINFHELYSKFISAIKNS------ 443 (1591)
T ss_pred ccccCCchhhhhhheeeechHhhhhhHHHHHHHHHHcChhhHHHHHHHHhhhhhhcccchHHHHHHHHHHHhCc------
Confidence 34568999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred HHHHHHHHHHHhcccccccChHHHHHHHHHHhhhhhhhhhcCccccccCCChhhHHHHHHhcCceeEEechhhhcccccc
Q 000444 118 VQATYENCKVLLGSELIKSSSEERSLLKNLGSWLGKLTIGRNQVLRAREIDPKSLIIEAYEKGLMIAVIPFTSKILEPCQ 197 (1498)
Q Consensus 118 l~~T~~~i~~LL~s~~~~~~s~eRs~LKNLG~WLG~iTlarnkPi~~k~l~~K~LLleaY~~g~L~~viPFVcKvLe~~~ 197 (1498)
+| -+||++|||||+|||.|||||||||++.++|||+||+|||++|||..|+|||||||+.|.
T Consensus 444 --~t----------------~~dk~~LKNLgsWLG~iTl~rNkPI~~l~l~~kslLlEaY~sg~ll~VvPFVaKIL~~as 505 (1591)
T KOG1831|consen 444 --VT----------------ESDKRLLKNLGSWLGEITLGRNKPIKELDLDFKSLLLEAYGSGRLLPVVPFVAKILEGAS 505 (1591)
T ss_pred --cc----------------hhHHHHHHHHHHHHHHHHHhcCCchHHhhhhHHHHHHHHhccCceeecchHHHHHHHhhh
Confidence 22 189999999999999999999999999999999999999999999999999999999999
Q ss_pred cCccccCCChhHHHHHHHHHHHhcCCCccchhHHHHHHHHhhcCCCccccccccccccchhhhcCCCCCCCCCcCCCCCC
Q 000444 198 SSLAYQPPNPWTMAILGLLAEIYSMPNLKMNLKFDIEVLFKNLGVDMKDITPTSLLKDRKREIEGNPDFSNKDVGASQPQ 277 (1498)
Q Consensus 198 ~SkvFkPPNPW~m~IL~lL~Ely~~~~lKlnLkFEIEvL~K~L~l~~~~i~ps~~L~~r~~~~~~~~d~~~~~~~~~q~~ 277 (1498)
+|+|||||||||||||++|+|||+.||||+|||||||||||+||+++++++|++++++..+. ++... .
T Consensus 506 ksrIFkpPnpW~~gIlklL~ELh~e~d~klnLkFEIEVLlkslN~~l~~le~~~~lnn~~~i-~~~L~-----------~ 573 (1591)
T KOG1831|consen 506 KSRIFKPPNPWTMGILKLLAELHQEADLKLNLKFEIEVLLKSLNVILSELEPSETLNNIIRI-KKQLV-----------L 573 (1591)
T ss_pred hccccCCCCchHHHHHHHHHHhcccccceeeeeeeeeehhccccchHhhcchhhHHhhHHhH-HHHHc-----------c
Confidence 99999999999999999999999999999999999999999999999999999999984431 11110 0
Q ss_pred ccCCCCccccCCCCCCCCCCCCCCCCCCCCCcccccccccccccccccchhHHHHhhccCCCCCCcccccccccCCCCCC
Q 000444 278 LVPEVKPAIVSPLGHVDLPLDVASPPNSGGPTHLLSQYAAPLRLSSGTLMEDEKLAALGISDQLPSAQGLFQASQSQSPF 357 (1498)
Q Consensus 278 ~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~l~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~ 357 (1498)
+.++.. +..+++ . .|...+.+ ...|
T Consensus 574 ~~~e~h-------~~~~~~-------------------------------------------~---~q~~~~~~--~~~f 598 (1591)
T KOG1831|consen 574 MKLETH-------QSLELE-------------------------------------------D---IQQVTLGN--TIAF 598 (1591)
T ss_pred CChhhc-------cccccC-------------------------------------------c---hhcccccC--Cccc
Confidence 000000 000000 0 00000000 1114
Q ss_pred ccccccCC-CCCCCceEEecccccccccchhhhhhHHHHHHHHHHhhhhhchhhhHHHHHHHHHHHHhhcccCChhhhHH
Q 000444 358 SVSQLSTP-IPNIGTHVIINQKLTALGLHLHFQRVVPIAMDRAIKEIVSGIVQRSVSIATQTTKELVLKDYAMESDETRI 436 (1498)
Q Consensus 358 s~~~~~~~-ip~l~~~v~in~~l~~f~~~p~LKriV~~Ai~rAIrEII~PVVERSVtIA~iTT~eLV~KDFA~E~DE~km 436 (1498)
++++.+.. ..+...++...| ||++|++|+.|++++|+|||.||||||+.||++||+.||+||||+|+||+||
T Consensus 599 a~~~~n~~t~~~~i~~l~~~~-------~P~~Kh~~~~Aleqsv~eii~~Vv~rs~~IA~ttTe~lirKDFA~e~~es~l 671 (1591)
T KOG1831|consen 599 AYDARNVSTATEVIKQLDLRP-------HPDIKHRVQEALEQSVVEIIEPVVERSSGIASTTTESLIRKDFALERDESRL 671 (1591)
T ss_pred eecccccchhhhhhhhccCCC-------CccHHHHHHHHHHHHHHHHHHHHHHHhhceeehhHHHHHHHHHhcccchhHH
Confidence 44444322 122223333333 8999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhhHHHchHHHHHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 000444 437 YNAAHLMVASLAGSLAHVTCKEPLRGSISSQLRNSLQGLTIASELLEQAVQLVTNDNLDLGCAVIEQAATDKAIQTIDGE 516 (1498)
Q Consensus 437 r~AAh~Mv~~LAgSLAlVTckEpLr~si~~~lr~~l~~~~~~~~~~e~~i~~~~~dNldLac~~Iekaa~ekA~~eId~~ 516 (1498)
|.||+.|||+||++||++||||||+++|+++|+..+.+.......+++++..+++||++++|++|||+|+|||++|||.+
T Consensus 672 ~~Aa~~M~r~la~~lAmiTcreplk~am~~nl~~~~~~~l~~~~ai~~a~~t~~~dNv~l~~~~Iek~a~eka~~dI~~~ 751 (1591)
T KOG1831|consen 672 RLAASQMVRELAAGLAMITCREPLKVAMSSNLVLAALSLLSLMAAIARAADTLQSDNVELVVKFIEKTAIEKATQDIDSR 751 (1591)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhHHHHHHHhhHHHHHhhhhHHHHHHHHHHHHHHhhchhhHhhhhHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999876665678899999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhhcC-CCCCcCcccccccccCCCCCCCCCCCCCChhHHHHhHhhhc-CCCCC-CCCCCCCccccCccCC
Q 000444 517 IAQQLSLRRKHREGV-GSSFFDPNIYAQGSMGVPEALRPKPGHLSVSQQRVYEDFVR-LPWQN-QSSQGSHAMSAGSLTS 593 (1498)
Q Consensus 517 l~~~~~~Rr~hre~~-~~~f~D~~~~s~~~~~LPe~LrlkpgGlt~~Ql~VYEdF~r-~p~~~-~~~~~~~~~~~s~~~~ 593 (1498)
|++++..|+.||+++ +.||+|.....+. ..||+++|+++||++|+|++|||+|+| +|+.. .++...+..
T Consensus 752 L~q~~~~Rv~~k~~~~~~~fvD~~~~~~~-~~LP~~vr~~~~~~~~~l~~vYe~F~k~i~~~~~~s~~~~la~------- 823 (1591)
T KOG1831|consen 752 LEQDICGRVFHKENPEVMPFVDLLSAAYS-CTLPEVVRLKIGGLTPQLFRVYEEFPKPIPGFLGNSSRKDLAE------- 823 (1591)
T ss_pred HHHhhHhheecccCCccccchhhhhhhhh-ccCcHhhhcccCCCCHHHHHHHHHcccccccccccCCCccccc-------
Confidence 999999999999965 8999999875554 449999999999999999999999998 33211 000000000
Q ss_pred CCchhhhhhccCCCCCCCCCCCCCCCCCCcccccCCccccCCCCccCcccccccchhcccCCCCCcccccccccccccCC
Q 000444 594 SGDAAQASAYGLAGGQGNQGYSSSAGSTGFDAVSRPSDVASGTTESTSAGFLSTSLVHIGAADGGILHNSESESVNAAFT 673 (1498)
Q Consensus 594 ~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~qp~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 673 (1498)
. .+++.++.+....+.. +.....++.+... +.+.....+.
T Consensus 824 -----------~--------------------~~~~~dlt~~~~~s~~---~~lv~~ei~~~~~------~~a~~~~i~~ 863 (1591)
T KOG1831|consen 824 -----------Y--------------------ITESSDLTQPHVISNA---LDLVVREICGAIV------EKACQTAIQT 863 (1591)
T ss_pred -----------c--------------------cCCCccccchhhhhHH---HHHHHHHHHHHHH------HHHHHHHHHh
Confidence 0 1111111100000000 0000000000000 0000000000
Q ss_pred hhhhhhhccCCCCCCCCCCCCCCCCCCCcccccccccccccccchhhhHHHHHHHHHHHHHHhhcCCcchhHHHHhhhhH
Q 000444 674 PAATELYAADSTEPVKEPGASSQSLPSTAAPERIGSSILEPSLQTRDALDKYHIVAQKLDALIGNDAREAEVQGVISEVP 753 (1498)
Q Consensus 674 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~le~~~~~~~~l~~l~~~~~~~~~i~~~i~~i~ 753 (1498)
+ .++.. ++++. ..|+.+- . + ...+..++.+..++. ..+.++++..+
T Consensus 864 ~----~l~~~----------a~s~~---~~m~~v~----~-----~---~~~~~~~~~~~~~~a-----r~i~hli~~~V 909 (1591)
T KOG1831|consen 864 G----MLQFK----------AQSVE---KLMEEVP----A-----R---NMVVNLVNSLLLLVA-----RSIEHLISGLV 909 (1591)
T ss_pred h----hhhhh----------hhcch---hhHHhcc----c-----h---hhhHHHHHHHHHHHH-----HHHHHHHHHHH
Confidence 0 00000 00000 0011110 0 0 000001111110000 01111111111
Q ss_pred HHHHhhcChhHHHHHHHHHHHHHHhcccCCcchHHHHHHHHHHHHHHhHH-HHHHHHhhhhccccccccCHHHHHHHHHh
Q 000444 754 EIILRCISRDEAALAVAQKVFKGLYENASNNLHFSAHLAILAAIRDVCKL-VVKELTSWVIYSDEERKFNRDITMGLIRS 832 (1498)
Q Consensus 754 ~~i~~~~~~d~~~l~~aq~vv~~L~~~~~~~l~~ev~~~lL~~L~~l~~~-~~kevt~wl~~s~d~rKfNv~vi~~Lir~ 832 (1498)
.. ..+.+...++ .+--.+++..+|+.+|....+ ..+.|+..+..+++++|||++.+..|++.
T Consensus 910 ~~--------------~~~~l~~~~~---~~~I~~i~m~iL~~ic~~~qk~~~~~vs~a~s~~~~~~e~n~~~~~~L~~~ 972 (1591)
T KOG1831|consen 910 SY--------------FMKNLELDFS---TEKIFKIIMEILDNICRFIQKAGVRKVSEAISSSRSSLEYNIEKAEHLILS 972 (1591)
T ss_pred HH--------------HHHHHHHhhc---chhHHHHHHHHHHHHHHhccHHHHHHHHHHHHhchHHHHhhHHHHHHHHHH
Confidence 00 0111111111 122346677888888988754 55568888889999999999999999999
Q ss_pred CCCChhhhHHHHHHHHhcCCChhhHHHHHHHHHHHhcCCchhhH---hhHHHHHHHHHHHHcCCCCh----hH----HHH
Q 000444 833 ELLNLAEYNVHMAKLIDGGRNKAATEFAISLLQTLVTDESRVVI---SELHNLVDALAKLAAKPGSP----ES----LQQ 901 (1498)
Q Consensus 833 ~Li~~~elD~~Lak~i~~~~n~~av~Fa~~Ll~~~l~~~~~~~~---~df~~tleaL~~~~~~~~~~----~~----~~~ 901 (1498)
+|++..++|.+|+++|++|.|..++.|+++|++....++..... ..|..|.|.+.|+.+...+. +. ...
T Consensus 973 ~l~~~~~vd~~l~~amDs~~n~~vi~f~iell~~~~~~dnvi~~~~~~~~~~t~E~~~ri~q~v~s~~~~~g~~~~~~~~ 1052 (1591)
T KOG1831|consen 973 LLLDSGHVDKHLAKAMDSGGNQEVIAFLIELLRIAYGGDNVIADEWKNLFKETKEELFRILQSVESSEDKSGECASLCDY 1052 (1591)
T ss_pred hccChhhHHHHHHHHhccCCChHHHHHHHHHHHHhccCcchhhhhhhhhhhhHHHHHHHHHHHHhcccccchhhhhHHHH
Confidence 99999999999999999999999999999999999888885542 45788999988864321110 00 011
Q ss_pred HHHHHhCcccccCCCCCCccccchhhhhhcccccccccccCcCCCCCCCCCCCCCCChHHHHHHHHHHHHHhhcCCCCCc
Q 000444 902 LIEIVRNPAANANASSGATTAKDDKARQSKDKKAYSHTTANREDYNIPESVDPDPVGFPEQVSMLFAEWYQICELPGSND 981 (1498)
Q Consensus 902 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dp~~l~eq~~~lF~EWV~l~~~~~~~d 981 (1498)
.++.+- + ++. +........+|+.++.||++.+|.|||.+|+.+..++
T Consensus 1053 ~v~~~~-------------------------k---~~s-----~~~~m~~~~~~~~~lt~K~~~v~~~Wv~L~~~~~~~~ 1099 (1591)
T KOG1831|consen 1053 IVEHAI-------------------------K---SGS-----SADFMFRRMDDKQKLTEKTEIVFLEWVILLNDSRKND 1099 (1591)
T ss_pred HHHhcc-------------------------C---CCC-----chhHHHHhcCcchhhhhHHHHHHHHHHHHHhccccch
Confidence 111110 0 000 0001123346778999999999999999999999999
Q ss_pred hhHHHHHHHHHHcCcccCCchhHHHHHHHHHHHHHHhhhccccCCCCCCCCCccccccc-hhHHHHHHHHHHHHhcCCCC
Q 000444 982 AACTRYVLQLHQNGLLKGDDMTDRFFRRLTEVSVAHCLSSEVINPGTLQSPQQSQSLSF-LAIDIYAKLMLSILKCCPVE 1060 (1498)
Q Consensus 982 ~~~~~Fi~qL~~~giL~~de~~~~FfR~~~E~sV~~~~~~~~~~~g~~~~~s~~~~~~f-~~iDA~akLIv~lik~~~~~ 1060 (1498)
...++||+||+++|||++||..++|||.|+|+||+.++.... .....+ ..++|+.+....+..|.+
T Consensus 1100 ~s~~~fi~ql~~~GVls~dd~ltqFfr~~~el~~~i~~~a~~-----------~~a~~~i~tv~~~~~~l~~l~~f~d-- 1166 (1591)
T KOG1831|consen 1100 ESLAAFIQQLNEIGVLSTDDLLTQFFRADLELCVVIFLEASL-----------ITALVQICTVYAFICTLEMLDGFVD-- 1166 (1591)
T ss_pred HHHHHHHHHHHHcCcccchHHHHHHHHhhhhhhHHHHHHhcc-----------cccchhhhhHHHHHHHHHHHHHHhc--
Confidence 999999999999999999999999999999999999985431 012222 578888888888888763
Q ss_pred CCCcHHHHHHHHHHHHHHHHHhhhhhhhcCCCCCchHHHHHHHHHhhcCCCCCCCcchHHHHHHHHHHhhhcCCCCCCch
Q 000444 1061 QGSSKIFLLSKILTVTVKFILKDAEEKKASFNPRPYFRLFINWLLDMSSLDPVADGSNFQILSAFANAFHVLQPLKVPAF 1140 (1498)
Q Consensus 1061 ~~~~k~~~L~kiL~ii~~vl~~dhe~~~~~FnqrpyfRlfs~LL~el~~~~~~~~~~~~~~l~~fa~~l~~lqP~~~PgF 1140 (1498)
+++|.+|++||+++|++|+++||+++|+.|||+||||+|+++|.||...+..++...++++++|+++||.|||.++|||
T Consensus 1167 -~~tk~dl~~KI~~livgv~akdHs~~~e~f~~~~y~Rlf~~ll~E~~~~~~~le~~~~~i~SaF~~tfhalqp~~~Pgf 1245 (1591)
T KOG1831|consen 1167 -LPTKIDLFNKILNLIVGVFAKDHSERGEYFNQCPYFRLFSMLLPELMTADSVLEPISLDILSAFKNTFHALQPRRFPGF 1245 (1591)
T ss_pred -CchHHHHHHHHHHHHHHHHhcchHHhhhhHhhCcHhHHHHHHHHHhccccchhhhHHHHHHHHHHHHHHHhCcccCccc
Confidence 3789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHhHhHhhhcccchHHhhcCCCCCChHHHHHHHHHHHHhhhhhhcCCCCCchHHHHHHhHHHHHHHHHhccchHHHHHhh
Q 000444 1141 SFAWLELVSHRSFMPKLLIGNGQKGWPYIQRLLVNLLQFLEPFLRNAELGVPVRFLYKGTLRVLLVLLHDFPEFLCDYHF 1220 (1498)
Q Consensus 1141 aFaWl~LISHR~F~p~lL~~~~~~gW~~~~~LL~~llkFl~~~l~~~~l~~~~~~lYkgtLRilLvLlHDfPeFL~~~h~ 1220 (1498)
+|||++|||||+|+|++|..+++|||+.|++|+++|||||+||+||.++.++++++|||||||+||++||||||||+|||
T Consensus 1246 ~fawL~lishr~li~~~L~~~~~k~~~~~~~llislfkfL~~ylrn~~~~k~~~~lykgTLrVilvllhDfp~fl~~~hy 1325 (1591)
T KOG1831|consen 1246 AFAWLELISHRGLIPRMLAETNQKGWPLYAQLLISLFKFLAPYLRNYELFKPVQLLYKGTLRVILVLLHDFPEFLCEYHY 1325 (1591)
T ss_pred ceeeeecccchhHHHHHHHhccccccHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHcchHHhhcccccchHHHHHhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhccCCCcccccccceecccCCCCCCCCCCCCCCCCCCCcCcCCCCccccchHHHHHHhhhhHHHHHHhccCCCCcchH
Q 000444 1221 TFCDVIPPSCIQMRNIILSAFPRNMRLPDPSTPNLKIDLLPEIRDPPRIFSEVDAALRAKQMRADVDDYLKTGQPGSSFL 1300 (1498)
Q Consensus 1221 ~lc~~iP~~ciQLRNiILSA~P~~~~LPDPf~p~lkvd~lpei~~~P~i~~d~~~~L~~~~lk~~vD~yl~~r~~~~~~l 1300 (1498)
.+||.||++|+||||+||||||++|++||||++|+|||.|||+..+|+|+++++. +.+...|+++|.|+++|.+. +|+
T Consensus 1326 ~~~~~iPp~cvqlrniilsafp~~m~lpdpf~~~lkve~lpe~~~ap~i~~~~~~-i~~~~~~~dl~a~l~s~~~~-t~l 1403 (1591)
T KOG1831|consen 1326 GLCDTIPPNCVQLRNIILSAFPSNMRLPDPFAVNLKVEMLPEGFYAPRILYSITQ-IMPSNFRKDLDARLKSSSPV-TFL 1403 (1591)
T ss_pred hccCCCCcHHHHHHHHHHHhccccCcCCCccccccchhhhhhhhcCchhcCCHHH-hcccccCCCHHHHhhccccH-hHH
Confidence 9999999999999999999999999999999999999999999999999999999 88899999999999998885 889
Q ss_pred HHHHHHcCCCccccccCCccccHhHHHHHHHHHHHHHHHhhhccCCcccccCCCCchhhhhhhhHHHHHHHHHhccChhh
Q 000444 1301 SELKQKLLLPPSEAASAGTRYNVPLINSLVLYVGMQAIHQLQTRTSHAQSTGNNSSLTAFLVSAALDIFQTLIQDLDTEG 1380 (1498)
Q Consensus 1301 ~~i~~~L~~~~~~~~~~g~~yn~~linalVLyvg~~ai~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ll~~L~~~ld~E~ 1380 (1498)
..++..++... ..|++||..+|||+|+|||++|+.+++++....+++ +++|+++|+|+++|+.+||+||
T Consensus 1404 ~~~~~~~~~~~----~~~~~~~~~~~naiVlyvG~~ai~~~~~~~~~~~~~-------~it~s~~~~i~~nL~~nld~e~ 1472 (1591)
T KOG1831|consen 1404 SCLPQLLQVIK----EPGTRYNNQLINAIVLYVGIQAIAHLRRKSQNPSTS-------TITHSAYMDIFQNLIVNLDTEG 1472 (1591)
T ss_pred HHhhHHHHHhc----CccccccHHHHHHHHHHHHHHHHHHHHhccCCCccc-------ccccCchhhHHHHHHHhcchhh
Confidence 98888776532 479999999999999999999999998766555443 4678999999999999999999
Q ss_pred HHHHHHHHHhhhcCCChhHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhccCCCCchHHHHHHHHHhhCCCCccccCCc
Q 000444 1381 RYLFLNAAANQLRYPNNHTHYFSFVLLYLYAEANQEIIQEQITRVLFERLIVNRPHPWGLLITFIELIKNPRYNFWNQSF 1460 (1498)
Q Consensus 1381 RY~ll~aianqLRYPN~HT~~Fs~~lL~LF~~~~~~~IqEqItRVLLERliv~rPHPWGLlitfiELikNp~Y~Fw~~~F 1460 (1498)
||++++||||||||||+|||||||++||||.+++...|||||||+++||+||||||||||+|||+||||||.||||+|||
T Consensus 1473 ry~~l~aianqlryp~~ht~~~s~~~l~lfk~~~~~pike~i~~~~lerii~nrPHpWGllitF~eLikN~~YNfw~~~f 1552 (1591)
T KOG1831|consen 1473 RYLLLNAIANQLRYPNSHTYYFSCVFLYLFKRAGNNPIKEQITRVLLERIIVNRPHPWGLLITFTELIKNPDYNFWDHPF 1552 (1591)
T ss_pred hHHHHHHHHHHhcCCchhhHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHhcCCCCCchhHHHHHHHHcCCCcccccCcc
Confidence 99999999999999999999999999999999988889999999999999999999999999999999999999999999
Q ss_pred CcchHHHHHHHHHHHHhcCCCCCCCc
Q 000444 1461 IRCAPEIEKLFESVARSCGGLKPVDD 1486 (1498)
Q Consensus 1461 vk~aPEIe~lF~sva~sc~~~~~~~~ 1486 (1498)
|+|+|||.+||++|+++|+....++.
T Consensus 1553 v~~~pEI~rlfqsl~~~~~~~s~s~~ 1578 (1591)
T KOG1831|consen 1553 VQCAPEIKRLFQSLAKYCKAYSTSEQ 1578 (1591)
T ss_pred cccCHHHHHHHHHHHHHhhCcccccc
Confidence 99999999999999999997765544
No 2
>COG5103 CDC39 Cell division control protein, negative regulator of transcription [Cell division and chromosome partitioning / Transcription]
Probab=100.00 E-value=1.1e-228 Score=2031.67 Aligned_cols=1199 Identities=29% Similarity=0.427 Sum_probs=985.3
Q ss_pred CCCCCHHhhhhhhhhcccCChhhHHHHHHHHHHHhhhcChhHHHHHHHhhhcccCcchhHHHHHHHHHhCChhHHHHHHH
Q 000444 40 IEAPASEVQDKISFIINNISALNVEAKAKEFTEILKEQYYPWFAQYMVMKRASIEPNFHDLYLKFLDKVNSKALNREIVQ 119 (1498)
Q Consensus 40 ~e~P~e~v~dki~Fi~NNls~~Nl~~K~~El~~~l~~~y~~WFa~YLV~~Ras~EpN~H~lY~~~l~~l~~~~L~~~il~ 119 (1498)
-|--+++|..+|+|.+||++.-|+..|++|+|+.|+|.|.+||+.|||.+|++.|||||+||.++++.++++.||..+.+
T Consensus 781 ~Eg~~~evV~~iLFaiNNl~~ln~n~ki~~lk~~Ltp~y~~wfs~y~vtqR~~~e~n~~~ly~kvve~lgS~dly~~~~r 860 (2005)
T COG5103 781 NEGRATEVVKSILFAINNLLDLNRNDKIHRLKEALTPGYVGWFSIYMVTQRSTAEENCRRLYGKVVERLGSKDLYLRFSR 860 (2005)
T ss_pred ccccHHHHHHHHHHHhhhHHhhhccchHHHHHHhcCcccccceeeEEEEeeccccchHHHHHHHHHHHhccchHHHHHHH
Confidence 45567788888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhcccccccChHHHHHHHHHHhhhhhhhhhcCccccccCCChhhHHHHHHhcCceeEEechhhhcccccccC
Q 000444 120 ATYENCKVLLGSELIKSSSEERSLLKNLGSWLGKLTIGRNQVLRAREIDPKSLIIEAYEKGLMIAVIPFTSKILEPCQSS 199 (1498)
Q Consensus 120 ~T~~~i~~LL~s~~~~~~s~eRs~LKNLG~WLG~iTlarnkPi~~k~l~~K~LLleaY~~g~L~~viPFVcKvLe~~~~S 199 (1498)
.|++.++.||+...- +++|+++|||||+|||+||||+||||+|+++|||++|+|||+.||+..|+|||||+|++++.|
T Consensus 861 ~TL~~l~~ll~~~~e--s~~ekk~lKnLgswLG~ItLa~NkpIt~~q~~Fk~~lve~~~~~Ri~~vvpFV~k~L~~as~s 938 (2005)
T COG5103 861 KTLEFLKMLLDYRCE--SPSEKKVLKNLGSWLGRITLAKNKPITSEQFDFKKFLVESVECRRILFVVPFVSKFLRQASCS 938 (2005)
T ss_pred HHHHHHHHHHhcccc--ChHHHHHHHHHHHHHhHHHHhhcCccccccccHHHHHHHHhhcCceEEeehHHHHHHHhcccc
Confidence 999999999998744 889999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCChhHHHHHHHHHHHhcCCCccchhHHHHHHHHhhcCCCccccccccccccchhhhcCCCCCCCCCcCCCCCCcc
Q 000444 200 LAYQPPNPWTMAILGLLAEIYSMPNLKMNLKFDIEVLFKNLGVDMKDITPTSLLKDRKREIEGNPDFSNKDVGASQPQLV 279 (1498)
Q Consensus 200 kvFkPPNPW~m~IL~lL~Ely~~~~lKlnLkFEIEvL~K~L~l~~~~i~ps~~L~~r~~~~~~~~d~~~~~~~~~q~~~~ 279 (1498)
+||||||||+||||+||.|||+++++||+||||||+|+|+||++++.|||++.++++.-.-. . .. +..
T Consensus 939 ~IFkPpNPW~mgILkLL~El~~~a~~~l~lkFEie~Ll~~lnv~~~~ikPs~~~~n~~V~ks-~---------LE--ke~ 1006 (2005)
T COG5103 939 IIFKPPNPWVMGILKLLSELHSCAPRVLRLKFEIEGLLRHLNVELVPIKPSKSLGNHLVLKS-R---------LE--KEL 1006 (2005)
T ss_pred eEecCCCchHHHHHHHHHHHHhcCcceeehhhhHHHHHHhcceeeccCChhhhhCcHHHHHH-H---------Hh--hhc
Confidence 99999999999999999999999999999999999999999999999999999987653100 0 00 111
Q ss_pred CCCCccccCCCCCCCCCCCCCCCCCCCCCcccccccccccccccccchhHHHHhhccCCCCCCcccccccccCCCCCCcc
Q 000444 280 PEVKPAIVSPLGHVDLPLDVASPPNSGGPTHLLSQYAAPLRLSSGTLMEDEKLAALGISDQLPSAQGLFQASQSQSPFSV 359 (1498)
Q Consensus 280 ~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~~l~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~s~ 359 (1498)
|+. + ++ ++.|.++ .+++||+.... ++. ..++. ++.-
T Consensus 1007 ~Ed----v--L~-a~~~d~~----------~~~~qyi~~~s-Sq~-TvtD~-va~~------------------------ 1042 (2005)
T COG5103 1007 PED----V--LN-AKFPDGT----------DYLAQYIIEDS-SQI-TVTDL-VARH------------------------ 1042 (2005)
T ss_pred hHH----H--Hh-hhccccc----------hHHHHHHHHhh-hcc-hHHHH-HHHH------------------------
Confidence 110 0 00 0111000 13334432100 000 00000 0000
Q ss_pred ccccCCCCCCCceEEecccccccccchhhhhhHHHHHHHHHHhhhhhchhhhHHHHHHHHHHHHhhcccCChhhhHHHHH
Q 000444 360 SQLSTPIPNIGTHVIINQKLTALGLHLHFQRVVPIAMDRAIKEIVSGIVQRSVSIATQTTKELVLKDYAMESDETRIYNA 439 (1498)
Q Consensus 360 ~~~~~~ip~l~~~v~in~~l~~f~~~p~LKriV~~Ai~rAIrEII~PVVERSVtIA~iTT~eLV~KDFA~E~DE~kmr~A 439 (1498)
...| -|.+|++.|+|++.+||||++.|||||+.||++||+.|++||||+|.|+.++..|
T Consensus 1043 --------------~g~P-------~PaiK~~~Qlal~~SVrEI~~aVVeks~gIAi~Tt~~l~~KDFa~ev~~s~l~~a 1101 (2005)
T COG5103 1043 --------------VGSP-------KPAIKNLTQLALDLSVREICGAVVEKSCGIAIQTTMALFKKDFAMEVEKSMLYVA 1101 (2005)
T ss_pred --------------cCCC-------ChHHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhccChhHHHHH
Confidence 0011 2899999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhhhHHHchHHHHHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 000444 440 AHLMVASLAGSLAHVTCKEPLRGSISSQLRNSLQGLTIASELLEQAVQLVTNDNLDLGCAVIEQAATDKAIQTIDGEIAQ 519 (1498)
Q Consensus 440 Ah~Mv~~LAgSLAlVTckEpLr~si~~~lr~~l~~~~~~~~~~e~~i~~~~~dNldLac~~Iekaa~ekA~~eId~~l~~ 519 (1498)
|++||++|||+||+|||+|||++.|.+++|++..++..-...+.+++..++++|+++||.+||+|+++|++++|+..++.
T Consensus 1102 ar~Mv~~La~~La~vT~~EPlk~~i~~n~rs~a~~l~sv~~~~ae~vd~~~~eN~~va~~lIe~a~~~k~~~~i~aei~h 1181 (2005)
T COG5103 1102 ARNMVVNLAKFLALVTAQEPLKACISGNVRSYAMKLCSVLDFSAEKVDKIAMENQDVACRLIERAGVSKVSESISAEIEH 1181 (2005)
T ss_pred HHHHHHHHHHHHHHHHhHhhHHHHHhccHHHHHHHHhhhhhchHHHHHHHHHhchhHHHHHHHHhhhhhhHHHHHHHHHH
Confidence 99999999999999999999999999999999887766567778889999999999999999999999999999999999
Q ss_pred HHHHHHHhhhcC-CCCCcCcccccccccCCCCCCCCCCCCCChhHHHHhHhhhcCCCCCCCCCCCCccccCccCCCCchh
Q 000444 520 QLSLRRKHREGV-GSSFFDPNIYAQGSMGVPEALRPKPGHLSVSQQRVYEDFVRLPWQNQSSQGSHAMSAGSLTSSGDAA 598 (1498)
Q Consensus 520 ~~~~Rr~hre~~-~~~f~D~~~~s~~~~~LPe~LrlkpgGlt~~Ql~VYEdF~r~p~~~~~~~~~~~~~~s~~~~~~~~~ 598 (1498)
++..||+||+++ ++||+|++. +.++++||++|+++-||+||||+++||||.|+|-..- ++|....+.-
T Consensus 1182 ~Iv~R~~Hrktt~n~PFvd~aa-a~~slnLps~L~ls~~~~Tpqqf~lyE~fD~l~ls~i---~~h~~~~~~n------- 1250 (2005)
T COG5103 1182 MIVERVRHRKTTPNLPFVDPAA-ANLSLNLPSSLELSIGKATPQQFSLYEDFDRLSLSTI---MGHIEKIAIN------- 1250 (2005)
T ss_pred HHHHHHHhhccCCCCCccCccc-CccccCCCcccccccCCcCHHHhhhhhcccccccccc---ccccchhhhh-------
Confidence 999999999976 899999996 6667899999999999999999999999998753222 2222211110
Q ss_pred hhhhccCCCCCCCCCCCCCCCCCCcccccCCccc-cCCCCccCcccccccchh-cccCCCCCcccccccccccccCChhh
Q 000444 599 QASAYGLAGGQGNQGYSSSAGSTGFDAVSRPSDV-ASGTTESTSAGFLSTSLV-HIGAADGGILHNSESESVNAAFTPAA 676 (1498)
Q Consensus 599 ~~~~~~~~~~~~~~~~~~~~q~~~~~~~~qp~~~-~~~~~~~~~~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~~p~~ 676 (1498)
+....++ ++++++ |.++ +..+ .-.+|++ ++.. . ... .+.+
T Consensus 1251 ---~~~Td~a---------dstdal-----~~nl~nt~e-------~eAnQta~~yq~--n----------~L~--i~~q 1292 (2005)
T COG5103 1251 ---AIDTDSA---------DSTDAL-----NNNLNNTVE-------NEANQTALEYQE--N----------LLI--IKAQ 1292 (2005)
T ss_pred ---hhcCChh---------hhhhhh-----ccccchhhh-------hHHHHHHHHHHH--H----------hhh--hhhH
Confidence 0000000 000000 0000 0000 0000000 0000 0 000 0000
Q ss_pred hhhhccCCCCCCCCCCCCCCCCCCCcccccccccccccccchhhhHHHHHHHHHHHHHHhhcCCcchhHHHHhhhhHHHH
Q 000444 677 TELYAADSTEPVKEPGASSQSLPSTAAPERIGSSILEPSLQTRDALDKYHIVAQKLDALIGNDAREAEVQGVISEVPEII 756 (1498)
Q Consensus 677 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~le~~~~~~~~l~~l~~~~~~~~~i~~~i~~i~~~i 756 (1498)
.-++ ..+.+.++++.+.+. .| |-. +.+ +. +.+..++.+|...|
T Consensus 1293 l~Ql------~~~~Py~~~~~V~aD--------------------~e--~~~---lkE-----~~-NQ~~t~~~~Il~~I 1335 (2005)
T COG5103 1293 LVQL------SKKIPYSSKKNVIAD--------------------EE--HGL---LKE-----GK-NQFETVFRRILESI 1335 (2005)
T ss_pred HHHh------cccCCcchhhcCcch--------------------hh--hhH---HHh-----hH-HHHHHHHHHHHHHh
Confidence 0000 011111111111110 11 110 111 11 35667778888777
Q ss_pred HhhcChhHHHHHHHHHHHHHHhcccCCcchHHHHHHHHHHHHHHhHHHHHHHHhhhhccccccccCHHHHHHHHHhCCCC
Q 000444 757 LRCISRDEAALAVAQKVFKGLYENASNNLHFSAHLAILAAIRDVCKLVVKELTSWVIYSDEERKFNRDITMGLIRSELLN 836 (1498)
Q Consensus 757 ~~~~~~d~~~l~~aq~vv~~L~~~~~~~l~~ev~~~lL~~L~~l~~~~~kevt~wl~~s~d~rKfNv~vi~~Lir~~Li~ 836 (1498)
.++ |+.++.++|.+++.|+..+.+++++||+.++||+||++|-+++|+|.||++|+.|.||||+|+|.+||++|||+
T Consensus 1336 a~s---d~~~l~c~q~c~~il~~~skSp~~~evls~~lEkic~~S~kt~k~V~~wl~ysnD~rKfnip~I~slie~nli~ 1412 (2005)
T COG5103 1336 ASS---DDKDLECIQLCRYILGHLSKSPSKEEVLSRCLEKICKISFKTQKEVLGWLIYSNDPRKFNIPLIGSLIEHNLIN 1412 (2005)
T ss_pred ccc---hhhHHHHHHHHHHHHhccccCchHHHHHHHHHHHHHhHhHHHhhhhheeeeecCChhhcCcHHHHHHHHhccch
Confidence 765 99999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhHHHHHHHHhcCCChhhHHHHHHHHHHHhcCCchh-hHhhHHHHHHHHHHHHcCCCChhHHHHHHHHHhCcccccCC
Q 000444 837 LAEYNVHMAKLIDGGRNKAATEFAISLLQTLVTDESRV-VISELHNLVDALAKLAAKPGSPESLQQLIEIVRNPAANANA 915 (1498)
Q Consensus 837 ~~elD~~Lak~i~~~~n~~av~Fa~~Ll~~~l~~~~~~-~~~df~~tleaL~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 915 (1498)
..|||.+|++.|.+.. +.+.|||+.|++..++++.++ ++.||.+|+|.|+.-. + +.++++.+.+.+...-
T Consensus 1413 ~~E~D~~l~r~i~~~~-gnvtdFai~Ll~~~V~~e~pi~~~~dFI~tLe~la~s~----d-~~vk~f~~~~~~tm~~--- 1483 (2005)
T COG5103 1413 VVEYDQALSRKIPLAD-GNVTDFAIALLASLVTAEVPICTVYDFICTLEMLAGSS----D-PKVKDFFQKISNTMMH--- 1483 (2005)
T ss_pred hhhHHHHHHhhccccc-cchHHHHHHHHHHHhccCCceeeHHHHHHHHHHHhccC----C-hhHHHHHHHHHHhhhh---
Confidence 9999999999998533 448999999999777766655 5699999999985432 2 4456666655421110
Q ss_pred CCCCccccchhhhhhcccccccccccCcCCCCCCCCCCCCCCChHHHHHHHHHHHHHhhcCCCCCchhHHHHHHHHHHcC
Q 000444 916 SSGATTAKDDKARQSKDKKAYSHTTANREDYNIPESVDPDPVGFPEQVSMLFAEWYQICELPGSNDAACTRYVLQLHQNG 995 (1498)
Q Consensus 916 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dp~~l~eq~~~lF~EWV~l~~~~~~~d~~~~~Fi~qL~~~g 995 (1498)
.+..| ....+.||+..+|.|||++.++...+|.....|+.||+++|
T Consensus 1484 ------------------~v~kg----------------nKqq~ndqi~iVf~ewv~llrn~~~nD~v~~~F~~ql~e~g 1529 (2005)
T COG5103 1484 ------------------IVAKG----------------NKQQLNDQIIIVFSEWVELLRNCRFNDTVPEMFLPQLMERG 1529 (2005)
T ss_pred ------------------ccccc----------------ccccccceEEEeeHHHHHHHHhcccccccHHHHHHHHHHcc
Confidence 00011 12456799999999999999999999999999999999999
Q ss_pred cccCCchhHHHHHHHHHHHHHHhhhccccCCCCCCCCCccccccchhHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHH
Q 000444 996 LLKGDDMTDRFFRRLTEVSVAHCLSSEVINPGTLQSPQQSQSLSFLAIDIYAKLMLSILKCCPVEQGSSKIFLLSKILTV 1075 (1498)
Q Consensus 996 iL~~de~~~~FfR~~~E~sV~~~~~~~~~~~g~~~~~s~~~~~~f~~iDA~akLIv~lik~~~~~~~~~k~~~L~kiL~i 1075 (1498)
+++.+++...|||+.+|.+|.+|... .+.+.+|..|||++.||+.++++.| ..+.++..|++||++.
T Consensus 1530 ~~s~~~~~~~ffk~sle~~i~aF~e~------------~pta~~y~~IDal~sLi~n~l~~eG-~te~T~s~~~~kii~~ 1596 (2005)
T COG5103 1530 DYSASLDIRSFFKVSLEHFIRAFHER------------IPTAYCYLKIDALPSLIKNRLYEEG-STEGTVSVLFRKIIKD 1596 (2005)
T ss_pred CCCchHHHHHHHHhhHHHHHHHHhhc------------CCcccceeeccchHHHHHHHHHHhc-cccchHHHHHHHHHHH
Confidence 99999999999999999999999743 2357899999999999999999964 4456778999999999
Q ss_pred HHHHHHhhhhhhhcCCCCCchHHHHHHHHHhhcCCCCCCCcchHHHHHHHHHHhhhcCCCCCCchhHhHhHhhhcccchH
Q 000444 1076 TVKFILKDAEEKKASFNPRPYFRLFINWLLDMSSLDPVADGSNFQILSAFANAFHVLQPLKVPAFSFAWLELVSHRSFMP 1155 (1498)
Q Consensus 1076 i~~vl~~dhe~~~~~FnqrpyfRlfs~LL~el~~~~~~~~~~~~~~l~~fa~~l~~lqP~~~PgFaFaWl~LISHR~F~p 1155 (1498)
|++|++++|..+++.||+|+||||||++|+||.......+++...+.+.|-++|..|||.+||||+|||++|+|||+.+|
T Consensus 1597 i~~VFae~h~~~~e~~h~~~fFrLfS~il~e~~dv~~~d~s~fv~~~Sv~y~~f~alqP~~fPgFtfawl~llSH~~llP 1676 (2005)
T COG5103 1597 ILFVFAEAHRKRAEFVHNYLFFRLFSRILIETLDVIDEDTSCFVNNRSVVYSIFEALQPSRFPGFTFAWLELLSHKFLLP 1676 (2005)
T ss_pred HHHHHHHHHHHhhhhhhcccHHHHHHHHHHHHhhhhhccchhhhhhHHHHHHHHHHcCcccCCchHHHHHHHHHhhhhhh
Confidence 99999999999999999999999999999999876544556677888999999999999999999999999999999999
Q ss_pred HhhcCCCCCChHHHHHHHHHHHHhhhhhhcCCCCCchHHHHHHhHHHHHHHHHhccchHHHHHhhhhhccCCCccccccc
Q 000444 1156 KLLIGNGQKGWPYIQRLLVNLLQFLEPFLRNAELGVPVRFLYKGTLRVLLVLLHDFPEFLCDYHFTFCDVIPPSCIQMRN 1235 (1498)
Q Consensus 1156 ~lL~~~~~~gW~~~~~LL~~llkFl~~~l~~~~l~~~~~~lYkgtLRilLvLlHDfPeFL~~~h~~lc~~iP~~ciQLRN 1235 (1498)
++|+.|+++||+.|..+|+++|||++ +++......++++|+|+||+.||++||||.||+++||++...+|+.|+||||
T Consensus 1677 ~vL~v~Nd~~~d~f~~~lmsflKFlD--~s~~~v~~~~~~ly~Gflr~iLv~~hD~P~FLit~~yql~~~~P~e~vqlrN 1754 (2005)
T COG5103 1677 KVLLVNNDKINDLFSEGLMSFLKFLD--LSEEGVVLVMEALYCGFLRTILVYLHDFPGFLITQIYQLFRRNPLECVQLRN 1754 (2005)
T ss_pred hhhhccchhhHHHHHHHHHHHHHHhc--chHHHHHHHHHHHHhcchheeeeeeccCchHHHHHHHHHhhcCCHHHHHHHH
Confidence 99999999999999999999999998 7778888999999999999999999999999999999999999999999999
Q ss_pred ceecccCCCCCCCCCCCCCCCCCCCcCcCCCCccccchHHHHHHhhhhHHHHHHhccCCCCcchHHHHHHHcCCCccccc
Q 000444 1236 IILSAFPRNMRLPDPSTPNLKIDLLPEIRDPPRIFSEVDAALRAKQMRADVDDYLKTGQPGSSFLSELKQKLLLPPSEAA 1315 (1498)
Q Consensus 1236 iILSA~P~~~~LPDPf~p~lkvd~lpei~~~P~i~~d~~~~L~~~~lk~~vD~yl~~r~~~~~~l~~i~~~L~~~~~~~~ 1315 (1498)
+||||||++|.+||||..||||..+|+|++.|.++.|+...| .++++.+| | |.+.++.+..+.+++....+...
T Consensus 1755 m~lSa~Psdlt~p~Pfa~~Lkv~~~P~~k~~p~~f~d~~v~l--e~~~s~~d--L--e~~~~S~l~~~~s~~~~d~y~~k 1828 (2005)
T COG5103 1755 MMLSAYPSDLTYPCPFAQGLKVQEYPHIKNFPNQFRDRIVPL--EGQNSFFD--L--EACLRSALQNRTSVKVTDLYIGK 1828 (2005)
T ss_pred HHHHhccccCcCCCchhcccccccChHhhhhhHHhcccccch--hhcccchh--h--HHHhhhhhhHHHHHHHHHhhccc
Confidence 999999999999999999999999999999999999988887 47888888 5 55555777777766654433322
Q ss_pred cCCcc---ccHhHHHHHHHHHHHHHHHhhhccCCcccccCCCCchhhhh-hhhHHHHHHHHHhccChhhHHHHHHHHHhh
Q 000444 1316 SAGTR---YNVPLINSLVLYVGMQAIHQLQTRTSHAQSTGNNSSLTAFL-VSAALDIFQTLIQDLDTEGRYLFLNAAANQ 1391 (1498)
Q Consensus 1316 ~~g~~---yn~~linalVLyvg~~ai~~~~~~~~~~~~~~~~~~~~~~~-~s~~~~ll~~L~~~ld~E~RY~ll~aianq 1391 (1498)
..|.. ++-..+-++|+|+|++++..... .|+ +|+.+.++..++..++++.||+++.||++|
T Consensus 1829 ~t~~~~~~~dn~~~~~~V~h~~~es~~~~~~---------------~f~~ks~~~t~l~~~~r~g~~~~rY~ll~ai~~q 1893 (2005)
T COG5103 1829 NTPLWVYLIDNLNEMDAVSHTVVESIKFMIE---------------RFMHKSEILTMLWIRMRAGGPPKRYFLLTAILAQ 1893 (2005)
T ss_pred cCceeeeeeccHHHHHHHHHHHhhhHHHHHH---------------HHhccccHHHHHHHHHhcCCCchhhHHHHHHHHH
Confidence 33322 24567889999999998653211 233 356899999999999999999999999999
Q ss_pred hcCCChhHHHHHHHHHHHhhccc----chhhHHHHHHHHHHHhccCCCCchHHHHHHHHHhhCCCCccccCCcCcchHHH
Q 000444 1392 LRYPNNHTHYFSFVLLYLYAEAN----QEIIQEQITRVLFERLIVNRPHPWGLLITFIELIKNPRYNFWNQSFIRCAPEI 1467 (1498)
Q Consensus 1392 LRYPN~HT~~Fs~~lL~LF~~~~----~~~IqEqItRVLLERliv~rPHPWGLlitfiELikNp~Y~Fw~~~Fvk~aPEI 1467 (1498)
|||||+|||||||++|++|.++. +-.||||||||||||+||||||||||+|||+||+||.+||||+|||||..|||
T Consensus 1894 lRYp~ihTy~fs~vfl~~fkS~~~N~QkL~ikE~m~t~lLeRII~NrPH~WGl~i~FTeLlkNeD~Nf~k~Pyikr~~EI 1973 (2005)
T COG5103 1894 LRYPEIHTYDFSRVFLKSFKSHGYNPQKLLIKEQMTTVLLERIICNRPHPWGLLITFTELLKNEDYNFWKHPYIKRNDEI 1973 (2005)
T ss_pred hcCCCcchhHHHHHHHHHHhhcCCChHHHHHHHHHHHHHHHHHHcCCCCcchhheeHHHHhcccccchhcCcccccCHHH
Confidence 99999999999999999998763 45799999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhcCCCCCCC
Q 000444 1468 EKLFESVARSCGGLKPVD 1485 (1498)
Q Consensus 1468 e~lF~sva~sc~~~~~~~ 1485 (1498)
.++|+++.+++|....+.
T Consensus 1974 ~~lfdsL~e~v~a~ssan 1991 (2005)
T COG5103 1974 CRLFDSLHEHVMAPSSAN 1991 (2005)
T ss_pred HHHHHHHHHHhhCccccc
Confidence 999999999999876443
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=2.1e-115 Score=1026.66 Aligned_cols=366 Identities=59% Similarity=1.055 Sum_probs=340.2
Q ss_pred HHHHhhcCCCC--CCCcch--HHHHHHHHHHhhhcCCCCCCchhHhHhHhhhcccchHHhhc-CCCCCChHHHHHHHHHH
Q 000444 1102 NWLLDMSSLDP--VADGSN--FQILSAFANAFHVLQPLKVPAFSFAWLELVSHRSFMPKLLI-GNGQKGWPYIQRLLVNL 1176 (1498)
Q Consensus 1102 ~LL~el~~~~~--~~~~~~--~~~l~~fa~~l~~lqP~~~PgFaFaWl~LISHR~F~p~lL~-~~~~~gW~~~~~LL~~l 1176 (1498)
||||||+..+. .++..+ .+++.+||++||.+||..||||+|||++|||||+|||+||+ .++++||+.|++||+++
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 57999995332 333334 59999999999999999999999999999999999999999 88999999999999999
Q ss_pred HHhhhhhhcCCCCCchHHHHHHhHHHHHHHHHhccchHHHHHhhhhhccCCCcccccccceecccCCCCCCCCCCCCCCC
Q 000444 1177 LQFLEPFLRNAELGVPVRFLYKGTLRVLLVLLHDFPEFLCDYHFTFCDVIPPSCIQMRNIILSAFPRNMRLPDPSTPNLK 1256 (1498)
Q Consensus 1177 lkFl~~~l~~~~l~~~~~~lYkgtLRilLvLlHDfPeFL~~~h~~lc~~iP~~ciQLRNiILSA~P~~~~LPDPf~p~lk 1256 (1498)
|+|+++|+|+.+++++++++||||||++|||+||||||||+||++||++||++|+||||+||||+|++|+|||||+||+|
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 000444 1257 IDLLPEIRDPPRIFSEVDAALRAKQMRADVDDYLKTGQPGSSFLSELKQKLLLPPSEAAS----AGTRYNVPLINSLVLY 1332 (1498)
Q Consensus 1257 vd~lpei~~~P~i~~d~~~~L~~~~lk~~vD~yl~~r~~~~~~l~~i~~~L~~~~~~~~~----~g~~yn~~linalVLy 1332 (1498)
||++|||+++|.|.+|++..|++.|||++||+||+++ ++.+++++|+++|+.++.+... .|++||+++|||+|+|
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 9999999999999999999999999999999999864 4559999999999998775542 5799999999999999
Q ss_pred HHHHHHHhhhccCCcccccCCCCchhhhhhhhHHHHHHHHHhccChhhHHHHHHHHHhhhcCCChhHHHHHHHHHHHhh-
Q 000444 1333 VGMQAIHQLQTRTSHAQSTGNNSSLTAFLVSAALDIFQTLIQDLDTEGRYLFLNAAANQLRYPNNHTHYFSFVLLYLYA- 1411 (1498)
Q Consensus 1333 vg~~ai~~~~~~~~~~~~~~~~~~~~~~~~s~~~~ll~~L~~~ld~E~RY~ll~aianqLRYPN~HT~~Fs~~lL~LF~- 1411 (1498)
||++|+.+.++++..+.+.+ +++++++|++|++++|+||||++++||||||||||+|||||||+||+||+
T Consensus 240 vg~~a~~~~~~~~~~~~f~~---------~s~~~~ll~~Li~~ld~E~RY~ll~aiaNqLRYPN~HT~~Fs~~lL~lF~~ 310 (379)
T PF04054_consen 240 VGIQAVAEAQKKSSAPSFNT---------KSPHVTLLSKLIHELDPEGRYYLLSAIANQLRYPNSHTHFFSCVLLNLFSS 310 (379)
T ss_pred HhHHHHHHHhccCCCccccc---------cChHHHHHHHHHHhCCHHHHHHHHHHHHHHcCCCchhHHHHHHHHHHHhcC
Confidence 99999987655444444432 36799999999999999999999999999999999999999999999999
Q ss_pred ---cccchhhHHHHHHHHHHHhccCCCCchHHHHHHHHHhhCCCCccccCCcCcchHHHHHHHHHHHHh
Q 000444 1412 ---EANQEIIQEQITRVLFERLIVNRPHPWGLLITFIELIKNPRYNFWNQSFIRCAPEIEKLFESVARS 1477 (1498)
Q Consensus 1412 ---~~~~~~IqEqItRVLLERliv~rPHPWGLlitfiELikNp~Y~Fw~~~Fvk~aPEIe~lF~sva~s 1477 (1498)
+.++++||||||||||||+||+|||||||+|||+||+|||+|+||++|||||+||||++|++|+||
T Consensus 311 ~~~~~~~~~IqEqItRVLLERliv~rPHPWGllitfiELikN~~y~f~~~pFik~~pEI~~~f~~~~~~ 379 (379)
T PF04054_consen 311 DMNDPNDEDIQEQITRVLLERLIVNRPHPWGLLITFIELIKNPKYNFWELPFIKCAPEIEKLFESLARH 379 (379)
T ss_pred CCCccchhhhHHHHHHHHHHHHhcCCCCCccHHHHHHHHHhCccCCcccCcccccCHHHHHHHHHHhcC
Confidence 556889999999999999999999999999999999999999999999999999999999999986
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=3.8e-47 Score=395.26 Aligned_cols=145 Identities=56% Similarity=0.809 Sum_probs=140.1
Q ss_pred chhhhhhHHHHHHHHHHhhhhhchhhhHHHHHHHHHHHHhhcccCChhhhHHHHHHHHHHHHHHhhhhHHHchHHHHHHH
Q 000444 385 HLHFQRVVPIAMDRAIKEIVSGIVQRSVSIATQTTKELVLKDYAMESDETRIYNAAHLMVASLAGSLAHVTCKEPLRGSI 464 (1498)
Q Consensus 385 ~p~LKriV~~Ai~rAIrEII~PVVERSVtIA~iTT~eLV~KDFA~E~DE~kmr~AAh~Mv~~LAgSLAlVTckEpLr~si 464 (1498)
||+||++|+.|+||||||||.|||||||+||++||++||+||||+|+||+|||+|||+||++||||||+||||||||.+|
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-cHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 000444 465 SSQLRNSLQGL-TI-ASELLEQAVQLVTNDNLDLGCAVIEQAATDKAIQTIDGEIAQQLSLRRKHRE 529 (1498)
Q Consensus 465 ~~~lr~~l~~~-~~-~~~~~e~~i~~~~~dNldLac~~Iekaa~ekA~~eId~~l~~~~~~Rr~hre 529 (1498)
.+|||+++++. .. .++.+|++++++++||+||||++|||+|+|||+++||+.|+++|+.||+|||
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=97.74 E-value=0.047 Score=72.67 Aligned_cols=240 Identities=22% Similarity=0.278 Sum_probs=155.9
Q ss_pred hhhhcCccccccCCChhhHHHHHHhcCceeEEechhhhcccccccCccccCCChhHHHHHHHHHHHhcCCCccchhHHHH
Q 000444 154 LTIGRNQVLRAREIDPKSLIIEAYEKGLMIAVIPFTSKILEPCQSSLAYQPPNPWTMAILGLLAEIYSMPNLKMNLKFDI 233 (1498)
Q Consensus 154 iTlarnkPi~~k~l~~K~LLleaY~~g~L~~viPFVcKvLe~~~~SkvFkPPNPW~m~IL~lL~Ely~~~~lKlnLkFEI 233 (1498)
+..+.++-+..-.-|.+.+-+.-.++-+....+-++.+-|++..--+||.+-|||.|.++-.+.+.|++. |.-
T Consensus 713 ~~~ai~~a~~t~~~dNv~l~~~~Iek~a~eka~~dI~~~L~q~~~~Rv~~k~~~~~~~fvD~~~~~~~~~-LP~------ 785 (1591)
T KOG1831|consen 713 LMAAIARAADTLQSDNVELVVKFIEKTAIEKATQDIDSRLEQDICGRVFHKENPEVMPFVDLLSAAYSCT-LPE------ 785 (1591)
T ss_pred HHHHHHHHHHHHHhhchhhHhhhhHHHHHHHHHHHHHHHHHHhhHhheecccCCccccchhhhhhhhhcc-CcH------
Confidence 4777777777778889999999999999999999999999999999999999999999999999999985 332
Q ss_pred HHHHhhcCCCccccccccccccchhhhcCCCCCCCCCcCCCCCCccCCCCccccCCCCCCCCCCCCCCCCCCCCCccccc
Q 000444 234 EVLFKNLGVDMKDITPTSLLKDRKREIEGNPDFSNKDVGASQPQLVPEVKPAIVSPLGHVDLPLDVASPPNSGGPTHLLS 313 (1498)
Q Consensus 234 EvL~K~L~l~~~~i~ps~~L~~r~~~~~~~~d~~~~~~~~~q~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 313 (1498)
-++++...+.|.-+ +- ..+ |.+. .|+ ++
T Consensus 786 -----~vr~~~~~~~~~l~-~v-Ye~------F~k~---------i~~-----------------------------~~- 813 (1591)
T KOG1831|consen 786 -----VVRLKIGGLTPQLF-RV-YEE------FPKP---------IPG-----------------------------FL- 813 (1591)
T ss_pred -----hhhcccCCCCHHHH-HH-HHH------cccc---------ccc-----------------------------cc-
Confidence 22332222222110 00 000 0000 000 00
Q ss_pred ccccccccccccchhHHHHhhccCCCCCCcccccccccCCCCCCccccccCCCCCCCceEEecccccccccchhhhhhHH
Q 000444 314 QYAAPLRLSSGTLMEDEKLAALGISDQLPSAQGLFQASQSQSPFSVSQLSTPIPNIGTHVIINQKLTALGLHLHFQRVVP 393 (1498)
Q Consensus 314 q~~~~~~~~~~~l~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~s~~~~~~~ip~l~~~v~in~~l~~f~~~p~LKriV~ 393 (1498)
|+ ...+++..++.=+..+ .-..++.
T Consensus 814 ----------------------~~--------------------------s~~~~la~~~~~~~dl-------t~~~~~s 838 (1591)
T KOG1831|consen 814 ----------------------GN--------------------------SSRKDLAEYITESSDL-------TQPHVIS 838 (1591)
T ss_pred ----------------------cc--------------------------CCCcccccccCCCccc-------cchhhhh
Confidence 00 0000000000000000 0123568
Q ss_pred HHHHHHHHhhhhhchhhhHHHHHHHHHHHHhhcccCChhhhHHHHHHHHHHHHHHhhhhHHHchHHHHHHHHHHHHHHhh
Q 000444 394 IAMDRAIKEIVSGIVQRSVSIATQTTKELVLKDYAMESDETRIYNAAHLMVASLAGSLAHVTCKEPLRGSISSQLRNSLQ 473 (1498)
Q Consensus 394 ~Ai~rAIrEII~PVVERSVtIA~iTT~eLV~KDFA~E~DE~kmr~AAh~Mv~~LAgSLAlVTckEpLr~si~~~lr~~l~ 473 (1498)
.+.+-..+||.+-.+|+....|..+.. +-.|-+.+++--. .--|.+|+-+++.|+..+.. +++.-.|..+.-....
T Consensus 839 ~~~~lv~~ei~~~~~~~a~~~~i~~~~-l~~~a~s~~~~m~--~v~~~~~~~~~~~~~~~~~a-r~i~hli~~~V~~~~~ 914 (1591)
T KOG1831|consen 839 NALDLVVREICGAIVEKACQTAIQTGM-LQFKAQSVEKLME--EVPARNMVVNLVNSLLLLVA-RSIEHLISGLVSYFMK 914 (1591)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhh-hhhhhhcchhhHH--hccchhhhHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Confidence 899999999999999999888888887 7777777776444 22367999999999988777 6666656555443222
Q ss_pred cCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Q 000444 474 GLTIASELLEQAVQLVTNDNLDLGCAVIEQAATDKAIQTI 513 (1498)
Q Consensus 474 ~~~~~~~~~e~~i~~~~~dNldLac~~Iekaa~ekA~~eI 513 (1498)
++. ...--+-|..++-++++.+|.+++|++..|...-|
T Consensus 915 ~l~--~~~~~~~I~~i~m~iL~~ic~~~qk~~~~~vs~a~ 952 (1591)
T KOG1831|consen 915 NLE--LDFSTEKIFKIIMEILDNICRFIQKAGVRKVSEAI 952 (1591)
T ss_pred HHH--HhhcchhHHHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence 111 11112236778889999999999999988665554
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=94.56 E-value=0.39 Score=52.40 Aligned_cols=179 Identities=21% Similarity=0.269 Sum_probs=118.7
Q ss_pred hhhhhhcccCChhhHHHHHHHHHHHhhhcChhHHHHH---HHhhhcccCcchhHHHHHHHHHhCC--hhHHHHHHHHHHH
Q 000444 49 DKISFIINNISALNVEAKAKEFTEILKEQYYPWFAQY---MVMKRASIEPNFHDLYLKFLDKVNS--KALNREIVQATYE 123 (1498)
Q Consensus 49 dki~Fi~NNls~~Nl~~K~~El~~~l~~~y~~WFa~Y---LV~~Ras~EpN~H~lY~~~l~~l~~--~~L~~~il~~T~~ 123 (1498)
.+|.-++|-+|++|++.-++|+.+..... .+...+ .+.+++-.+|++-.+|..++..++. +.+-..+++.++.
T Consensus 2 ~~v~~~lnkLs~~n~~~~~~~l~~~~~~~--~~~~~~l~~~i~~~~~~~~~~~~~ya~L~~~l~~~~~~f~~~ll~~~~~ 79 (200)
T smart00543 2 KKVKGLINKLSPSNFESIIKELLKLNNSD--KNLRKYILELIFEKAVEEPNFIPAYARLCALLNAKNPDFGSLLLERLQE 79 (200)
T ss_pred hHHHHHHhhCCHHHHHHHHHHHHHHHccC--HHHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46788999999999999999999888653 334444 3567789999999999999999986 5677778888877
Q ss_pred HHHHHhcccccccChHHHHHHHHHHhhhhhhhhhcCccccccCCChhhHHHHHHhcCce------eEEechhhhcccccc
Q 000444 124 NCKVLLGSELIKSSSEERSLLKNLGSWLGKLTIGRNQVLRAREIDPKSLIIEAYEKGLM------IAVIPFTSKILEPCQ 197 (1498)
Q Consensus 124 ~i~~LL~s~~~~~~s~eRs~LKNLG~WLG~iTlarnkPi~~k~l~~K~LLleaY~~g~L------~~viPFVcKvLe~~~ 197 (1498)
.....+... ...++...+|+-.+||.+..-.=-+.. .+.+++-+--+...- ..-+=.+|.+|+.|.
T Consensus 80 ~f~~~~e~~----~~~~~~~~~~~i~fl~eL~~~~~i~~~----~i~~~l~~ll~~~~~~~~~~~~~~ve~l~~lL~~~G 151 (200)
T smart00543 80 EFEKGLESE----EESDKQRRLGLVRFLGELYNFQVLTSK----IILELLKELLNDLTKLDPPRSDFSVECLLSLLPTCG 151 (200)
T ss_pred HHHHHHHHH----HHHhhhhHHhHHHHHHHHHHcccCcHH----HHHHHHHHHHhccCCCCCCCcHHHHHHHHHHHHHhh
Confidence 766554433 335667778888888888765544322 122222222222110 134445678888876
Q ss_pred cCccccCCChhHH-HHHHHHHHHhcCC---CccchhHHHHHHHHh
Q 000444 198 SSLAYQPPNPWTM-AILGLLAEIYSMP---NLKMNLKFDIEVLFK 238 (1498)
Q Consensus 198 ~SkvFkPPNPW~m-~IL~lL~Ely~~~---~lKlnLkFEIEvL~K 238 (1498)
..--+ +.+|=.| .++..+....... .+....+|-+|-|+.
T Consensus 152 ~~l~~-~~~~~~~~~~l~~l~~~~~~~~~~~~~~r~~~~l~~l~~ 195 (200)
T smart00543 152 KDLER-EKSPKLLDEILERLQDYLLKKDKTELSSRLRFMLELLIE 195 (200)
T ss_pred HHHcC-cccHHHHHHHHHHHHHHHhcccccCCChHHHHHHHHHHH
Confidence 65433 5555444 4556665555555 577777888887765
No 7
>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=91.97 E-value=0.17 Score=55.27 Aligned_cols=188 Identities=18% Similarity=0.198 Sum_probs=113.4
Q ss_pred hhhhhcccCChhhHHHHHHHHHHHhhhcChhHHHHH---HHhhhcccCcchhHHHHHHHHHhCC--h-hHHHHHHHHHHH
Q 000444 50 KISFIINNISALNVEAKAKEFTEILKEQYYPWFAQY---MVMKRASIEPNFHDLYLKFLDKVNS--K-ALNREIVQATYE 123 (1498)
Q Consensus 50 ki~Fi~NNls~~Nl~~K~~El~~~l~~~y~~WFa~Y---LV~~Ras~EpN~H~lY~~~l~~l~~--~-~L~~~il~~T~~ 123 (1498)
||.-++|-+|+.|+++-++++.+..... ..+...+ ++.++|..+|++..+|..++..+.. + .+-..+++.+..
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 4455544 3467799999999999999999873 3 556666666666
Q ss_pred HHHHHh-cccccccChHHHHHHHHHHhhhhhhhhhcCccccccCCChhhHHHHHHhcC---ceeEEechhhhcccccccC
Q 000444 124 NCKVLL-GSELIKSSSEERSLLKNLGSWLGKLTIGRNQVLRAREIDPKSLIIEAYEKG---LMIAVIPFTSKILEPCQSS 199 (1498)
Q Consensus 124 ~i~~LL-~s~~~~~~s~eRs~LKNLG~WLG~iTlarnkPi~~k~l~~K~LLleaY~~g---~L~~viPFVcKvLe~~~~S 199 (1498)
.+.... ..+.......++...+++..+||.+....=-+-..-.--++.|+-.+.+.. .-..-|-.+|.+|..|...
T Consensus 82 ~f~~~~~~~~~~~~~~~~~~~~~~~~~fl~eL~~~~vv~~~~i~~~l~~ll~~~~~~~~~~~~~~~ie~~~~lL~~~G~~ 161 (209)
T PF02854_consen 82 EFEERYSNEELEENRQSSKQRRRGNIRFLAELFNFGVVSEKIIFDILRELLSDGTDECQPPPDEENIECLCTLLKTCGKK 161 (209)
T ss_dssp HHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHTSHHCCHHTCHHHHHHHHHHHHHHHHH
T ss_pred HHHHhhhhhhHHHHHHHHHHHHhhhhhHHHhhHhhccccchhHHHHHHHHHhcccccccCCCcHhHHHHHHHHHHHHHHH
Confidence 554411 012223456778889999999999886543221100012233333332211 1113344455555555433
Q ss_pred ccccCCC-hhHHHHHHHHHHHhcC---CCccchhHHHHHHHHh
Q 000444 200 LAYQPPN-PWTMAILGLLAEIYSM---PNLKMNLKFDIEVLFK 238 (1498)
Q Consensus 200 kvFkPPN-PW~m~IL~lL~Ely~~---~~lKlnLkFEIEvL~K 238 (1498)
--=.+.+ .=.-.++..+.+.... +++.-.++|=|+-+++
T Consensus 162 l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~r~~~~l~~l~~ 204 (209)
T PF02854_consen 162 LENSEESPKALDEIFERLQKYANSKKDPNLSSRIRFMLEDLIE 204 (209)
T ss_dssp HHHCHHHHHHHHHHHHHHHHHHHHCHSSSSSHHHHHHHHHHHH
T ss_pred HhcCCCchhHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHHH
Confidence 1100212 2233455555555555 5677777777776654
No 8
>KOG1467 consensus Translation initiation factor 2B, delta subunit (eIF-2Bdelta/GCD2) [Translation, ribosomal structure and biogenesis]
Probab=83.84 E-value=3.6 Score=50.89 Aligned_cols=112 Identities=21% Similarity=0.251 Sum_probs=83.3
Q ss_pred HHHHHHHHHHHhhcccCChhhhHHHHHHHHHHHHHHhhhhHHHchHHHHHHHHHHHHHHhhc---CC---Cc---HHHHH
Q 000444 413 SIATQTTKELVLKDYAMESDETRIYNAAHLMVASLAGSLAHVTCKEPLRGSISSQLRNSLQG---LT---IA---SELLE 483 (1498)
Q Consensus 413 tIA~iTT~eLV~KDFA~E~DE~kmr~AAh~Mv~~LAgSLAlVTckEpLr~si~~~lr~~l~~---~~---~~---~~~~e 483 (1498)
-||.+-+-+.|.|||-|++.. +-.|.|...+.+-+++-|---||-.||.|.+|-+=.. +. ++ .+.+-
T Consensus 256 CIa~L~afqevi~Dy~TP~~k----tlsrdLt~~i~~qv~~L~~cRPLs~SmgNAiRflK~eI~~L~~s~~e~eaKe~L~ 331 (556)
T KOG1467|consen 256 CIAMLQAFQEVIKDYTTPPEK----TLSRDLTAAISPQVSFLTQCRPLSISMGNAIRFLKNEISKLPISLSESEAKEELQ 331 (556)
T ss_pred HHHHHHHHHHHHHhccCCCcc----ccchhhHhhhhhHHHHHhhcCCccchhhHHHHHHHHHHhhCCCCCChHHHHHHHH
Confidence 399999999999999999877 4667888888888887665589999999999976322 22 11 34455
Q ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHhh
Q 000444 484 QAVQLVTNDNLDLGCAVIEQAATDKAI-----------QTIDGEIAQQLSLRRKHR 528 (1498)
Q Consensus 484 ~~i~~~~~dNldLac~~Iekaa~ekA~-----------~eId~~l~~~~~~Rr~hr 528 (1498)
..|..-+++++.+|-..|-+.|.+|.- .-++..|..+.+.+++.|
T Consensus 332 ~~I~~~i~eki~~A~qaI~q~a~~KI~dgdviltyg~s~vV~~ill~A~~~~k~fr 387 (556)
T KOG1467|consen 332 SDIDRFIAEKIILADQAISQHAVTKIQDGDVLLTYGSSSVVNMILLEAKELGKKFR 387 (556)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEEEecchHHHHHHHHHHHHhCcceE
Confidence 567888999999999999999988753 234555666555444443
No 9
>COG5088 SOH1 Rad5p-binding protein [General function prediction only]
Probab=35.78 E-value=87 Score=31.40 Aligned_cols=89 Identities=22% Similarity=0.299 Sum_probs=67.4
Q ss_pred hhHHHHHHHHHHHhhhcChhHHHHHHHhhhcccCcchhHHHHHHHHHhCChhHHHHHHHHHHHHHHHHhcccccccChHH
Q 000444 61 LNVEAKAKEFTEILKEQYYPWFAQYMVMKRASIEPNFHDLYLKFLDKVNSKALNREIVQATYENCKVLLGSELIKSSSEE 140 (1498)
Q Consensus 61 ~Nl~~K~~El~~~l~~~y~~WFa~YLV~~Ras~EpN~H~lY~~~l~~l~~~~L~~~il~~T~~~i~~LL~s~~~~~~s~e 140 (1498)
+-++-.++=+.-+-.+.|..|+++.=. -|-..-.-|++.++---+|..-++|+--+..-+-.||++......-+|
T Consensus 15 sRFE~ELEFvQ~L~Np~Yl~~Ltq~~~-----fese~F~~YL~YlEYWr~PeYs~fivYP~CL~iL~lLn~~~~~~~vs~ 89 (114)
T COG5088 15 SRFEVELEFVQSLANPQYLTLLTQQQI-----FESENFKNYLKYLEYWRNPEYSQFIVYPNCLFILKLLNGFMESAIVSE 89 (114)
T ss_pred chhHHHHHHHHHhcCHHHHHHHHHhhh-----hcCHHHHHHHHHHHHhhCCcccceeechhHHHHHHHhcchhHhhhhhh
Confidence 455555544455556889998886432 244445679999999999999999988888888889998877777788
Q ss_pred HHHHHHHH-----hhhhhh
Q 000444 141 RSLLKNLG-----SWLGKL 154 (1498)
Q Consensus 141 Rs~LKNLG-----~WLG~i 154 (1498)
-.++|.|| -|||+.
T Consensus 90 ~~l~~~l~e~qy~~Wlnk~ 108 (114)
T COG5088 90 DGLLEGLDELQYPQWLNKM 108 (114)
T ss_pred hHHHHhhhHHHHHHHHHHH
Confidence 89999998 477764
No 10
>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=31.19 E-value=80 Score=38.38 Aligned_cols=61 Identities=25% Similarity=0.453 Sum_probs=42.9
Q ss_pred ChHHHHHHHHHHHHhhhhhhcCCCCCchHHHHHHhHHHHHHHH------------HhccchHHHHHhhhhhccCCCcccc
Q 000444 1165 GWPYIQRLLVNLLQFLEPFLRNAELGVPVRFLYKGTLRVLLVL------------LHDFPEFLCDYHFTFCDVIPPSCIQ 1232 (1498)
Q Consensus 1165 gW~~~~~LL~~llkFl~~~l~~~~l~~~~~~lYkgtLRilLvL------------lHDfPeFL~~~h~~lc~~iP~~ciQ 1232 (1498)
-|..+..+|-+++++.+||-. ..++|+||+.+-.. .+|||+||-. .+.++.-
T Consensus 127 ~l~~v~~~l~~~lr~fGpF~s--------~~IikSTLdFv~g~~iEq~nf~~~p~A~~fP~ylR~-----ksGl~E~--- 190 (357)
T cd00686 127 WWALVNEHFPNVLRHFGPFCS--------LNLIRSTLDFFEGCWIEQYNFGGFPGSHDYPQFLRR-----MNGLGHC--- 190 (357)
T ss_pred HHHHHHHHHHHHHHHhhhhhH--------HHHHHHHHHHHHHHHHhhhccCCCCCCcccchHHHh-----ccCCcce---
Confidence 477788888888888888876 56889999886544 2488888743 3444433
Q ss_pred cccceecccCCC
Q 000444 1233 MRNIILSAFPRN 1244 (1498)
Q Consensus 1233 LRNiILSA~P~~ 1244 (1498)
.-.+.||+.
T Consensus 191 ---yA~FiFPk~ 199 (357)
T cd00686 191 ---VGASLWPKE 199 (357)
T ss_pred ---eEEEecchh
Confidence 356778875
No 11
>KOG3091 consensus Nuclear pore complex, p54 component (sc Nup57) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=22.58 E-value=9.6e+02 Score=30.82 Aligned_cols=27 Identities=22% Similarity=0.404 Sum_probs=23.3
Q ss_pred hhcccCChhhhHHHHHHHHHHHHHHhh
Q 000444 424 LKDYAMESDETRIYNAAHLMVASLAGS 450 (1498)
Q Consensus 424 ~KDFA~E~DE~kmr~AAh~Mv~~LAgS 450 (1498)
.+-|++.+||++||+=...|-+.|-+=
T Consensus 404 ~~G~~L~~~EE~Lr~Kldtll~~ln~P 430 (508)
T KOG3091|consen 404 KRGYALTPDEEELRAKLDTLLAQLNAP 430 (508)
T ss_pred ccCCcCCccHHHHHHHHHHHHHHhcCh
Confidence 568999999999999999998877643
No 12
>cd05133 RasGAP_IQGAP1 IQGAP1 is a homodimeric protein that is widely expressed among vertebrate cell types from early embryogenesis. Mammalian IQGAP1 protein is the best characterized member of the IQGAP family, and contains several protein-interacting domains. Human IQGAP1 is most similar to mouse Iqgap1 (94% identity) and has 62% identity to human IQGAP2. IQGAP1 binds and cross-links actin filaments in vitro and has been implicated in Ca2+/calmodulin signaling, E-cadherin-dependent cell adhesion, cell motility, and invasion. Yeast IQGAP homologues have a role in the recruitment of actin filaments, are components of the spindle pole body, and are required for actomyosin ring assembly and cytokinesis. Furthermore, IQGAP1 over-expression has also been detected in gastric and colorectal carcinomas and gastric cancer cell lines.
Probab=21.55 E-value=9.9e+02 Score=29.64 Aligned_cols=42 Identities=21% Similarity=0.339 Sum_probs=31.8
Q ss_pred HHHHhhhhhchhhhHHHHHHHHHHHHhhcccCChhhhHHHHHHHHHHHHHHh
Q 000444 398 RAIKEIVSGIVQRSVSIATQTTKELVLKDYAMESDETRIYNAAHLMVASLAG 449 (1498)
Q Consensus 398 rAIrEII~PVVERSVtIA~iTT~eLV~KDFA~E~DE~kmr~AAh~Mv~~LAg 449 (1498)
+..|++++|+|.+-+ -.||.-+|.|..++.++..+=...=+|
T Consensus 54 ~yLk~vL~p~I~~ii----------e~~dLdlE~dP~~Iy~~~in~~E~~tG 95 (360)
T cd05133 54 NALRQILAPVVKEIM----------DDKSLNIKTDPVDIYKSWVNQMESQTG 95 (360)
T ss_pred HHHHHHHHHHHHHHh----------cCcccCccCCHHHHHHHHHHHHHHhcC
Confidence 457888888887722 378999999999999998765544445
No 13
>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]
Probab=21.38 E-value=2.4e+03 Score=29.92 Aligned_cols=96 Identities=16% Similarity=0.147 Sum_probs=54.8
Q ss_pred HHHHHHHhcccCCcch-HHHHHHHHHHHHHHhHHHHHHHH-------hhhhcccc-----ccccCHHHHHHHHHhCCCCh
Q 000444 771 QKVFKGLYENASNNLH-FSAHLAILAAIRDVCKLVVKELT-------SWVIYSDE-----ERKFNRDITMGLIRSELLNL 837 (1498)
Q Consensus 771 q~vv~~L~~~~~~~l~-~ev~~~lL~~L~~l~~~~~kevt-------~wl~~s~d-----~rKfNv~vi~~Lir~~Li~~ 837 (1498)
.++++.||...-.++. +-.|+.+...|....+.++.++. .|.++.-+ .+--+|-.|.-|.+.+++..
T Consensus 461 krLvKal~~vprt~ldllPyYsRlVAtl~~~M~dvat~lv~~L~~eFr~~~hkK~q~~ietk~~~VrfIsEL~KF~lv~~ 540 (1128)
T KOG2051|consen 461 KRLVKALFVVPRTRLDLLPYYSRLVATLSKCMPDVATELVTMLRKEFRSHLHKKAQINIETKLKIVRFISELCKFQLVPK 540 (1128)
T ss_pred HHHHHhhhcccchhhhhhhHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhHHhhhhhCccCh
Confidence 3688999977444443 23344444444443333443333 34444432 22234666777899999988
Q ss_pred hhhHHHHHHHHhcCCChhhHHHHHHHHHHH
Q 000444 838 AEYNVHMAKLIDGGRNKAATEFAISLLQTL 867 (1498)
Q Consensus 838 ~elD~~Lak~i~~~~n~~av~Fa~~Ll~~~ 867 (1498)
.+.=.-|=.+|. ......||.+..|+..|
T Consensus 541 ~~if~cLk~ll~-dF~~hnIEm~c~lLE~~ 569 (1128)
T KOG2051|consen 541 FEIFSCLKMLLN-DFTHHNIEMACVLLESC 569 (1128)
T ss_pred HHHHHHHHHHHH-hcccccHHHHHHHHHhc
Confidence 776666655554 23334488888888643
Done!