Query 004909
Match_columns 724
No_of_seqs 245 out of 447
Neff 5.8
Searched_HMMs 46136
Date Thu Mar 28 14:53:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004909.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004909hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0988 RNA-directed RNA polym 100.0 1E-128 3E-133 1120.6 46.5 692 3-721 127-843 (1145)
2 PF05183 RdRP: RNA dependent R 100.0 3E-102 6E-107 896.4 22.0 424 268-723 1-440 (579)
3 cd01213 tensin Tensin Phosphot 47.9 79 0.0017 30.8 7.6 86 262-379 47-133 (138)
4 TIGR00489 aEF-1_beta translati 39.2 83 0.0018 28.3 5.8 60 323-385 18-77 (88)
5 PRK00435 ef1B elongation facto 36.8 94 0.002 28.0 5.8 59 323-384 18-76 (88)
6 cd00292 EF1B Elongation factor 35.4 95 0.0021 27.9 5.6 55 323-380 18-72 (88)
7 PF01316 Arg_repressor: Argini 22.6 4E+02 0.0086 22.9 6.9 59 549-617 11-69 (70)
8 COG5207 UBP14 Isopeptidase T [ 21.2 7.7E+02 0.017 29.3 10.7 94 507-624 555-669 (749)
9 PHA02770 hypothetical protein; 18.6 1.1E+02 0.0023 26.0 2.6 19 339-361 46-65 (81)
10 PHA02097 hypothetical protein 17.0 1.3E+02 0.0028 24.5 2.5 28 406-433 30-59 (59)
No 1
>KOG0988 consensus RNA-directed RNA polymerase QDE-1 required for posttranscriptional gene silencing and RNA interference [RNA processing and modification]
Probab=100.00 E-value=1.3e-128 Score=1120.55 Aligned_cols=692 Identities=36% Similarity=0.479 Sum_probs=580.4
Q ss_pred eEEEEEec---ccceEEEcccceEEEEEEeecCe-eEEEEEeccchhhhhhcCCCCCc----ccEEEEEEccCCeEEEec
Q 004909 3 KFAVLWRG---VNVTVNFGFGMRKINFLLSHLGE-EYRLELDYENIWEIELHCPRWQM----TKYLLIQLLGAPRIFQKG 74 (724)
Q Consensus 3 ~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~-~~k~~~~~~~i~~~~~~~~~~~~----~~~~~~~l~~~P~i~~~~ 74 (724)
.|..+|.+ ..+.|+.....+.+.+.+...+. ++..|++++.+-+...++.+..+ .+....-..+.|.+++..
T Consensus 127 ~~~~~~~~~v~~~v~V~~~~~~~~~~~p~~~~~~~~v~f~~~~~~~i~~~~~D~~~~s~~~~~~~~~~~~~G~~k~~~~~ 206 (1145)
T KOG0988|consen 127 TFDCLESYKVNDQVTVRGSPVRRIVESPVVEYCKLCVPFEHSCRVLIETVSLDLDKPSIIRYPKSRRYLDNGGSKYFRFA 206 (1145)
T ss_pred eecceEEEeecceEEEeccceeeeeecccccccccccchhhcchhheeeEEeccCcchhccCcchhhhhhcCccceeecc
Confidence 58889999 99999999999999999766444 77777777766654444333322 111112225666666664
Q ss_pred CCCCCccccCccccccccCC-CCCceEeeccCCCCCccceeeEEEEecCCCCcchHHHhhhhcccc-----cc--eeeee
Q 004909 75 IRSPDLLYESPVFNFFKEVP-DDQWVRTTDFTPSNFIGQSTGLCMELPYRLELPDFKENFAYYKES-----ED--RFVLE 146 (724)
Q Consensus 75 ~~~~~~~~~~~~~~~~~~~~-~~~w~R~~df~~~~~ig~~~~~~l~~~~~~~~~~~~~~~~~~~~~-----~~--~~~~~ 146 (724)
..|.+-.+.++.+.+.+++. +++|+|++||++..++|+++++|++++.+ +.++++|++.. .. .+..+
T Consensus 207 ~~p~~~~~~~~~~Ef~k~~~~~~~~i~~~~~~~~~~v~~eta~~~eI~~~-----i~~~lP~~r~~~~~~~~~~~s~~ir 281 (1145)
T KOG0988|consen 207 FSPLLLALGDSELEFKKDFLADLLYIRTTDLRSRTGVGIETASCDEIRVP-----IWKDLPYNRYNGSTAEEFRLSVWIR 281 (1145)
T ss_pred cccHHHhhccceeeeecccccccceeeecceeccccccceeeccceecch-----hhccCCcccccccchhhhhhhhhee
Confidence 44444444444677677766 88999999999999999999999999874 44444555443 12 24456
Q ss_pred cCCccc-cCCCcccccCC-CCCCCCCcchHHHHHHHHHcCccCcccccHHHHHhhCCCCCCCChHHHHHHHHHHHhcccc
Q 004909 147 TGSAYS-RSLDLVPIVGP-PDGIALPYEILFKINLLVQNGCVAGPLLDSNFYRLVDPYRAPVSISCIEHALDKLYHLKEC 224 (724)
Q Consensus 147 ~~~~~~-~~~~~~~~~~~-~~~~~lpf~v~fql~~lv~~g~l~~~~~~~~f~~~l~~~~~~~~~~~~~~al~~l~~~~~~ 224 (724)
.|..|. ++.+++|+... ..++..+++.+++.++||+.|.+.......+|+.++..... .....++++||+|.+...+
T Consensus 282 ~~~~~~~~~~~~~~l~~~~~~git~~~e~l~~r~slv~dq~~~~~~~~~~f~~l~~~~~~-~d~~v~~a~LekL~~~~~~ 360 (1145)
T KOG0988|consen 282 LGSKYDVSSAQLVPLNDERDFGITHLYECLVSRGSLVKDQVLLEEAHLLEFLGLLRHKVL-GDDNVLEAKLEKLLKLSTK 360 (1145)
T ss_pred cccccccccceeeeccccccccceeehhhhhcccchhhhhHHhhhhHHHHHHHHHhhhhc-cchhHHHHHHHHHhhhhhh
Confidence 777776 34456777663 34677899999999999999999999999999999976433 1125566789999999999
Q ss_pred ccCchhHHHHHHHHhhhcCCCCCCCCccCCCCcEEEEEEEEcCCeeeeccccccccCceecccCCCCCcEEEEEEecCCC
Q 004909 225 CYEPSRWLTDQYRKYMTSRSKPSSPAISLDDGLVYVHRVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDL 304 (724)
Q Consensus 225 ~~dp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~v~iTPtri~l~~P~~e~sNRvlR~y~~~~d~FLRV~F~DE~~ 304 (724)
||||.-+.+..++...++.++ .+...+.+|+.+|++|.|||||+|+.+||++++|||+|+|..+.++||||+|+||++
T Consensus 361 cfd~~~~~k~i~~~~~~ng~~--~~~~~~~~g~~~vrk~v~TPtrv~~~~PE~~~gNRVlR~f~~~~t~~lRvtF~De~~ 438 (1145)
T KOG0988|consen 361 CFDPYCQYKKIAKLNPSNGKL--VTTKEIMEGLRRVRKVVFTPTRVYLLAPEVEMGNRVLRKFDKDSTRFLRVTFRDEDN 438 (1145)
T ss_pred hhhHHHHHHHHHHHhcccCcc--ccchhhhhcceeEEEEEEcCceeEecCchhhhcchhheeccccCceEEEEEEEcccc
Confidence 999999988887765555542 233456799999999999999999999999999999999999999999999999999
Q ss_pred cccccCCCCCCCCCCccchhhhHHHHHHHHHhcCeEEcceeEEEEeecCCCCCcceEEEEEeCCCCCHHHHHHHhcCCCc
Q 004909 305 DKIHSTDLSPRGSSATDITRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFRE 384 (724)
Q Consensus 305 ~~l~~~~~~pr~~~~~~~~~~~i~~Rv~~~L~~Gi~I~gR~y~FLafS~SqLR~~s~wFfa~~~~lt~~~Ir~wmGdF~~ 384 (724)
+ +..+++++ ..++.+|.||..+|++||.||+|+|+||||||||||+||.||++.....++++||.|||+|++
T Consensus 439 ~-~~ir~~S~-------~~~t~l~~rv~~~L~~Gi~v~~r~y~FL~~s~sQlRdngy~m~~~s~~~~i~~iR~wmG~F~~ 510 (1145)
T KOG0988|consen 439 K-LKIRTLST-------GSRTKLDMRVNSYLTDGISVANRRYEFLAFSNSQLRDNGYFMARFSDKTKIEDIREWMGDFRD 510 (1145)
T ss_pred c-cccccCCc-------chhhHHHHHHHHHHhcccEEccceeEEEEecccccccCceEEeecCCCccHHHHHHHhcchhh
Confidence 6 44433321 226899999999999999999999999999999999999998887777899999999999999
Q ss_pred ccCHHHHHHHhccccCCCccceee-ecCcEEEeCCeeccccCcceeeccccccccHHHHHHHHHHcCCCCCCCeEEEEee
Q 004909 385 IRNVAKYAARLGQSFSSSKETLSV-HMDEIEIIPDVKIEIGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRY 463 (724)
Q Consensus 385 i~~vaK~aARlgq~FSsT~~tv~v-~~~~i~~i~DI~~~~~g~~~~FTDG~G~IS~~lA~~I~~~l~l~~~~PSAfQiR~ 463 (724)
|.|++|||||||||||+|+.|..+ +..++..+|||+..++|++||||||||+||.++|++|++++++...+||||||||
T Consensus 511 i~nv~K~aARmGqCFs~Sr~T~~~~~~~~~~~~~DI~~g~~g~~y~FSDGvG~iS~~~a~~vsq~~~~~~~vPsaFQiR~ 590 (1145)
T KOG0988|consen 511 IDNVPKLAARMGQCFSQSRGTGYVLERLDRMCPPDIEGGKRGNNYCFSDGVGMISLQFAREVSQKRKFGKAVPSAFQIRY 590 (1145)
T ss_pred ccCHHHHHhhcCcceeccccccccccccccccCCcccccccCCceeecCCcccccHHHHHHHHHHHcccccCChheeeec
Confidence 999999999999999999999877 5667889999997777889999999999999999999999999888999999999
Q ss_pred cCceEEEEeCCCCCcceeeccccccccCCCCcEEEEeecCcccccccHHHHHHHhcCCCChHHHHHHHHHHHHHH--HHH
Q 004909 464 GGYKGVVAADPTSSKKLSLRDSMRKYESELTKLDVLAWSKYQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQL--DAI 541 (724)
Q Consensus 464 gG~KGvl~vdp~~~~~I~lR~Sm~KF~s~~~~LeI~~~S~~~p~~LNRQ~I~iLs~lGV~devF~~lq~~~l~~l--~~~ 541 (724)
||+||||+|||.....+.+|.||.||.|.+..++|+.|++++||+||||+|++|+.+||++++|+++|+..+++- ...
T Consensus 591 ~G~KGVvav~Ps~~~~~~~~~~~~~s~S~n~~~~v~~~~~f~~~~lnr~lI~Lls~~gv~n~~F~~il~~vle~~r~~~n 670 (1145)
T KOG0988|consen 591 GGYKGVVAVDPSMDKVLKLRDSMNKSQSFNSLLEVTPSSKFQPAFLNRQLITLLSYLGVLNKPFINILDQVLEKQRRITN 670 (1145)
T ss_pred cCCcceEEeCccHhhhhhhhhhhhhhhhhcceeeeeeccCCccccccHHHHHHHHhcCccchHHHHHHHHHHHHHHhhhh
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999943 344
Q ss_pred hcCHHHHHHHHHhcCCCCcHHHHHHHHHCCCCCCCchHHHHHHHHHHHHHHHhhccccceeecCceeeeeeeCCCCCCCC
Q 004909 542 LTDPLKAQEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNY 621 (724)
Q Consensus 542 l~d~~~a~~~l~~~~~~~~~~~l~~ml~~Gf~p~~epfl~~~L~~~~~~~L~~Lk~K~RI~Vp~s~~L~GV~DetG~L~~ 621 (724)
+.....++++|......+.+++++.++..++.++.|||+++||..++++.++.+|+|.||||+.|++||||+||||+||+
T Consensus 671 ~~e~~~~~~~l~~~~~m~~en~a~~~l~~~~~~D~EPflr~mL~~~~k~~~~~~kek~ripv~~Gr~lmGvvDETG~L~y 750 (1145)
T KOG0988|consen 671 RIEELLDRAALNYGEQMDDENIAAMILKGFPRIDSEPFLRSMLSSLLKFTLQLLKEKIRIPVDLGRSLMGVVDETGILKY 750 (1145)
T ss_pred hhhHHHHHHHhhhhhhccchHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHhcccccCcCCceeEeeecccccccc
Confidence 45555566777654445666766666666666888999999999999999999999999999999999999999999999
Q ss_pred CcEEEEEeCCccccccCCCccccccccccceeEeeEEEEEeCCCCCCCceEEEEeeeCCCCccCCCeEEeCCCCCCCccc
Q 004909 622 GQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQGLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRYILT 701 (724)
Q Consensus 622 gEVfvq~s~~~~~~~~~~~~~~~~~~~~~~~vi~G~VlV~RnP~lHPGDIrvv~AV~~P~L~hL~dvIVFp~kG~Rpl~s 701 (724)
||||||++.+.... ...+..+++|+|+||||||||||||||++||++|+|+||+|||||||||+||||+
T Consensus 751 gQVfVq~t~~~~~~-----------~~~~~~vitG~VlvtKNPcLhpGDVRVl~AV~vp~L~h~~dvVvFPQkGpRphpd 819 (1145)
T KOG0988|consen 751 GQVFVQYTKTIRNS-----------DSGRKEVITGKVLVTKNPCLHPGDVRVLKAVYVPALEHMVDVVVFPQKGPRPHPD 819 (1145)
T ss_pred CeEEEEEccccccc-----------ccCCceEEEeeEEEecCCCCCCCceEEEEeeccHHHHhhcCEEEcCCCCCCCCcc
Confidence 99999999862111 1122479999999999999999999999999999999999999999999999999
Q ss_pred ccCCC----ceEEEecccCcCCCc
Q 004909 702 MLKPR----LLWYELNSSHALPRF 721 (724)
Q Consensus 702 ~LSGg----~~~~~~~~~~~~p~~ 721 (724)
+|||| |.|-++||+.++|.+
T Consensus 820 E~aGsDLDGDeYfViWDqkLL~~~ 843 (1145)
T KOG0988|consen 820 EMAGSDLDGDEYFVIWDQKLLPPR 843 (1145)
T ss_pred ccccCCCCCceEEEEeChhhccCc
Confidence 99998 559999999999976
No 2
>PF05183 RdRP: RNA dependent RNA polymerase; InterPro: IPR007855 This entry represents various eukaryotic RNA-dependent RNA polymerases (RDRP; 2.7.7.48 from EC), such as RCRP-1, RDRP-2 and RDRP-6. These enzymes are involved in the amplification of regulatory microRNAs during post-transcriptional gene silencing []; they are also required for transcriptional gene silencing. Double-stranded RNA has been shown to induce gene silencing in diverse eukaryotes and by a variety of pathways []. These enzymes also play a role in the RNA interference (RNAi) pathway, which is important for heterochromatin formation, accurate chromosome segregation, centromere cohesion and telomere function during mitosis and meiosis. RDRP enzymes are highly conserved in most eukaryotes, but are missing in archaea and bacteria. The core catalytic domain of RDRP enzymes is structurally similar to the beta' subunit of DNA-dependent RNA polymerases (DDRP), however the other domains of DDRP show no similarity to those of RDRP.; GO: 0003968 RNA-directed RNA polymerase activity; PDB: 2J7O_A 2J7N_A.
Probab=100.00 E-value=2.6e-102 Score=896.41 Aligned_cols=424 Identities=44% Similarity=0.725 Sum_probs=303.5
Q ss_pred CeeeeccccccccCceecccCCCCCcEEEEEEecCCCcccccCCCCCCCCCCccchhhhHHHHHHHHHhcCeEEcceeEE
Q 004909 268 SRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATDITRTRIYTRILSTLRNGILIGDRKFE 347 (724)
Q Consensus 268 tri~l~~P~~e~sNRvlR~y~~~~d~FLRV~F~DE~~~~l~~~~~~pr~~~~~~~~~~~i~~Rv~~~L~~Gi~I~gR~y~ 347 (724)
||++|.||++|.|||++|+|++ |+||||+|+||++..+..+. ..+++|++++|++||.|+||+|+
T Consensus 1 ~r~~l~~p~~~~snr~~R~fg~--~~Flrv~f~d~~~~~~~~~~-------------~~~~~~~~~~l~~gi~i~~~~y~ 65 (579)
T PF05183_consen 1 TRIILEPPELEKSNRVLRRFGS--DRFLRVSFPDENSSSLRFSP-------------RVLGRRIRKFLKNGIKIGGRHYR 65 (579)
T ss_dssp --EEE---EEEE-BHHHHHH-G--GGEEEEEEE-TT---SSS-T-------------TSTTEEEEEEEEEE---------
T ss_pred CeEEEECCEecCCCceeEEeCC--CCEEEEEEEcCCCCcccccc-------------hhHHHHHHHHHhccceECcEEEE
Confidence 7899999999999999999966 68999999999987765321 11667889999999999999999
Q ss_pred EEeecCCCCCcceEEEEEeC----CCCCHHHHHHHhcCCCcccCH-HHHHHHhccccCCCccceeeecCcEEEeCCeecc
Q 004909 348 FLAFSSSQLRESSAWMFASR----YGLTAAEIREWMGNFREIRNV-AKYAARLGQSFSSSKETLSVHMDEIEIIPDVKIE 422 (724)
Q Consensus 348 FLafS~SqLR~~s~wFfa~~----~~lt~~~Ir~wmGdF~~i~~v-aK~aARlgq~FSsT~~tv~v~~~~i~~i~DI~~~ 422 (724)
|||+|+||+|+|+|||+|++ ..+++++|++|||+|++++++ +|++||||||||+|.+++.+++++|..+|||.
T Consensus 66 fl~~S~sqlr~~~~~f~~~~~~~~~~~~~~~i~~~~g~~~~~~~~~~K~~aRl~l~fS~T~~~~~i~~~~~~~i~Di~-- 143 (579)
T PF05183_consen 66 FLGFSNSQLRDHSCWFFAEDDGDRPPLTVEDIRNWMGDFSNIQSIPAKYAARLGLCFSSTVPTVVIPPDEIEVIPDIT-- 143 (579)
T ss_dssp ----------EEEEEEEEEE----B---HHHHHHHHH-GGGTSBH-HHHHHTTHHHHSB-EEEEE--GGGEE-SS--T--
T ss_pred EeecCCccccCCeEEEEecCCccCCcccHHHHHHhcccccccccHHHHHHHHHHHhccCccceEEecccceEEcCCcC--
Confidence 99999999999999999988 679999999999999998886 99999999999999999999999999999993
Q ss_pred ccCcceeeccccccccHHHHHHHHHHcCCCCCCCeEEEEeecCceEEEEeCCCC-Ccceeeccccccc----cCCCCcEE
Q 004909 423 IGKTKYVFSDGIGKVSAEFARKVASKCGLKDNPPSAFQIRYGGYKGVVAADPTS-SKKLSLRDSMRKY----ESELTKLD 497 (724)
Q Consensus 423 ~~g~~~~FTDG~G~IS~~lA~~I~~~l~l~~~~PSAfQiR~gG~KGvl~vdp~~-~~~I~lR~Sm~KF----~s~~~~Le 497 (724)
++++|+||||||+||+++|++||+++++ ..+|||||||+|||||||+|||+. +.+|.|||||+|| ++.+++||
T Consensus 144 -~~~~~~ftDG~G~IS~~la~~I~~~l~~-~~~PsA~QiR~~G~KGml~vdp~~~~~~I~lr~Sm~Kf~~~~~~~~~~le 221 (579)
T PF05183_consen 144 -SRNGYVFTDGCGRISPDLARKIAEKLGL-DYVPSAFQIRIGGAKGMLVVDPTLDGPWIQLRPSMIKFDEPWDSEHRTLE 221 (579)
T ss_dssp -TSS--BSSTTEEEE-HHHHHHHHHHHT--SS--SEEEEEETTEEEEEEE-TT-----EEE-TTTB-S----SGGGSEEE
T ss_pred -CCCCccccCCchhhCHHHHHHHHHHcCC-CCCCeEEEEeccCceeEEEECCCCCcceEEEehhhhhhccCcccccCeEE
Confidence 3678999999999999999999999997 889999999999999999999998 5899999999999 77889999
Q ss_pred EEeecC-cccccccHHHHHHHhcCCCChHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhcCCCCcHHHHH-HHHHCCCCCC
Q 004909 498 VLAWSK-YQPCFLNRQLISLLSTLGIWDEIFEKKQREAVRQLDAILTDPLKAQEALELMSPGENTNILK-ELLICGYKPD 575 (724)
Q Consensus 498 I~~~S~-~~p~~LNRQ~I~iLs~lGV~devF~~lq~~~l~~l~~~l~d~~~a~~~l~~~~~~~~~~~l~-~ml~~Gf~p~ 575 (724)
|+++|+ +.+++||||+|++|+++|||+++|+++|+++++++..+++++..|.++++............ .|+.+||++.
T Consensus 222 i~~~s~~~~~~~LN~q~I~iL~~~gv~~~~f~~l~~~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ll~~g~~~~ 301 (579)
T PF05183_consen 222 IVKYSRPPRPAYLNRQLITILEDLGVPDEVFLELQDEALEELRNILTDPDAARDLLSNQSRDGDFRLIRRQLLDAGFDPL 301 (579)
T ss_dssp EEEE--------B-TTTHHHHHHTBSS-HHHHHHHHHHHHHHHHHTTSHHHHHHHHHHHS--HHHHHHHTHHHHTT--TT
T ss_pred ecccCCCCCcccccHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHhcCCCcchhHHHHHHHHcCCCcc
Confidence 999998 89999999999999999999999999999999999999999999999998765544444333 8999999999
Q ss_pred CchHHHHHHHHHHHHHHHhhccccceeecCceeeeeeeCCCCCCCCCcEEEEEeCCccccccCCCccccccccccceeEe
Q 004909 576 AEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETRTLNYGQVFVQISGAGYRQLHGESSLFSSSRSRQRFIVQ 655 (724)
Q Consensus 576 ~epfl~~~L~~~~~~~L~~Lk~K~RI~Vp~s~~L~GV~DetG~L~~gEVfvq~s~~~~~~~~~~~~~~~~~~~~~~~vi~ 655 (724)
++||++.+++.+.++.++++|+|+||+||+|++||||+||||+|+|||||+|++... .++....+++
T Consensus 302 ~~pfl~~~l~~~~~~~l~~~~~~~ri~v~~s~~l~gv~D~~g~L~~geV~~~~s~~~-------------~~~~~~~~~~ 368 (579)
T PF05183_consen 302 NDPFLRSLLKALIKKKLKELKKKARIPVPKSRYLMGVPDPTGVLKEGEVFVQFSSDE-------------ETGSQSQVLE 368 (579)
T ss_dssp TBHHHHHHHHHHHHHHHHHHHHC--B--SSEEEEEEEE-TTS---TTEEEEEEEEEE-------------EETTEEEEEE
T ss_pred cCHHHHHHHHHHHHHHHHhccceEEEEcCCCcEEEEeeCCcCCCCCCEEEEEecccc-------------ccCCCcceee
Confidence 999999999999999999999999999999999999999999999999999997221 1123366999
Q ss_pred eEEEEEeCCCCCCCceEEEEeeeCCCCccCCCeEEeCCCCCCCcccccCCC----ceEEEecccCcCCCccc
Q 004909 656 GLVVVAKNPCLHPGDVRVLKAVNVPALHHMVDCVVFPQKGMRYILTMLKPR----LLWYELNSSHALPRFIV 723 (724)
Q Consensus 656 G~VlV~RnP~lHPGDIrvv~AV~~P~L~hL~dvIVFp~kG~Rpl~s~LSGg----~~~~~~~~~~~~p~~~~ 723 (724)
|+|+|+||||+||||||+|+||++|+|+||+||||||++|+||+|++|||| |.++++||+.||..|.+
T Consensus 369 g~VlV~R~P~~~pgDir~~~av~~p~L~~l~~vIVF~~~G~r~~~~~lsGgDlDGD~~~V~wd~~lv~~~~~ 440 (579)
T PF05183_consen 369 GDVLVTRNPCLHPGDIRKVKAVDKPELRHLKDVIVFSTKGDRPLPSELSGGDLDGDEYFVCWDPRLVEPFKN 440 (579)
T ss_dssp -EEEEE-SS--SGGGEEEEEE---GGGTT--SEEEE-S-SSS-HHHHTTT--SSS-EEEEE--HHHHHTB--
T ss_pred eeEEEecCCccCcCceeEEEeeccHHHcccCCEEEeCCCCCCCchHHhcCCCCCCceEEEEeCHhhhhhhhc
Confidence 999999999999999999999999999999999999999999999999995 66999999999766543
No 3
>cd01213 tensin Tensin Phosphotyrosine-binding (PTB) domain. Tensin Phosphotyrosine-binding (PTB) domain. Tensin is a a focal adhesion protein, which contains a C-terminal SH2 domain followed by a PTB domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=47.92 E-value=79 Score=30.81 Aligned_cols=86 Identities=17% Similarity=0.246 Sum_probs=56.0
Q ss_pred EEEEcCCeeeeccccccccCceecccCCCCCcEEEEEEecCCCcccccCCCCCCCCCCccchhhhHHHHHHHHHhcCeEE
Q 004909 262 RVQVTPSRVYFCGPEINVSNRVLRHFRRDIDNFLRISFIDEDLDKIHSTDLSPRGSSATDITRTRIYTRILSTLRNGILI 341 (724)
Q Consensus 262 ~v~iTPtri~l~~P~~e~sNRvlR~y~~~~d~FLRV~F~DE~~~~l~~~~~~pr~~~~~~~~~~~i~~Rv~~~L~~Gi~I 341 (724)
++.|+..+|.+..|.-.. -..|+|+.+ .|+|+.-+.+.-.+ +..|-..
T Consensus 47 h~kVS~qGItLtDn~rk~--ffrrhypl~-----~Vs~ca~dp~n~~~-------------------------~~~~~~~ 94 (138)
T cd01213 47 HFKVSSQGITLTDNTRKK--FFRRHYKVD-----SVIFCAIDPEERMW-------------------------ENEGAIA 94 (138)
T ss_pred EEEEEcCCeeeeccccce--eehhhCCcC-----eEEEEeeCCccccc-------------------------ccccccc
Confidence 788889999887754311 123456653 68888766442111 1122122
Q ss_pred cceeEEEEeecCCCCCcceEEEEEe-CCCCCHHHHHHHh
Q 004909 342 GDRKFEFLAFSSSQLRESSAWMFAS-RYGLTAAEIREWM 379 (724)
Q Consensus 342 ~gR~y~FLafS~SqLR~~s~wFfa~-~~~lt~~~Ir~wm 379 (724)
..|.|-|.+-...+..++.|+-|++ +....+..|.+..
T Consensus 95 ~kriFgFVar~~~~~~~~~ChvF~e~~~~qpa~~iv~~~ 133 (138)
T cd01213 95 KARIFAFVARIPHSSTDNACHVFAELEPEQPASAIVNFA 133 (138)
T ss_pred ccEEEEEEEecCCCCCCeeEEEeccCCCCCCHHHHHHHH
Confidence 6688889887766667899999997 4567888887764
No 4
>TIGR00489 aEF-1_beta translation elongation factor aEF-1 beta. This model describes the archaeal translation elongation factor aEF-1 beta. The member from Sulfolobus solfataricus was demonstrated experimentally. It is a dimer that catalyzes the exchange of GDP for GTP on aEF-1 alpha.
Probab=39.23 E-value=83 Score=28.33 Aligned_cols=60 Identities=13% Similarity=0.128 Sum_probs=45.7
Q ss_pred hhhhHHHHHHHHHhcCeEEcceeEEEEeecCCCCCcceEEEEEeCCCCCHHHHHHHhcCCCcc
Q 004909 323 TRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFREI 385 (724)
Q Consensus 323 ~~~~i~~Rv~~~L~~Gi~I~gR~y~FLafS~SqLR~~s~wFfa~~~~lt~~~Ir~wmGdF~~i 385 (724)
..+.+.++++.++.+|..+++-..+.+||+ |+.=.+.+.-++.....+.|-+-+..+...
T Consensus 18 Dle~L~~~ik~~~~~g~~~~~~~~ePiaFG---LkaL~~~~vv~D~~g~td~lee~i~~ve~V 77 (88)
T TIGR00489 18 DLEALKEKIKERIPEGVEIRKIDEEPIAFG---LVAINVMVVMGDAEGGTEAAEESLSGIEGV 77 (88)
T ss_pred CHHHHHHHHHHhCcCCcEEeeeEEEeeecc---ceeeEEEEEEecCCcChHHHHHHHhcCCCc
Confidence 478899999999999999999999999998 444346665666555568877776665543
No 5
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=36.80 E-value=94 Score=28.01 Aligned_cols=59 Identities=17% Similarity=0.188 Sum_probs=45.3
Q ss_pred hhhhHHHHHHHHHhcCeEEcceeEEEEeecCCCCCcceEEEEEeCCCCCHHHHHHHhcCCCc
Q 004909 323 TRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMGNFRE 384 (724)
Q Consensus 323 ~~~~i~~Rv~~~L~~Gi~I~gR~y~FLafS~SqLR~~s~wFfa~~~~lt~~~Ir~wmGdF~~ 384 (724)
....+.+.++.++.+|+.+++-..+.+||+ |+.=.+.+.-++.....+.+-+-+..+..
T Consensus 18 Dl~~L~~~ik~~~~~g~~~~~~~~ePIaFG---LkaL~i~~vv~D~~~~td~lee~i~~~e~ 76 (88)
T PRK00435 18 DLDELKEKIKEVLPEGYKINGIEEEPIAFG---LKALKLYVIMPDEEGGTEPVEEAFANVEG 76 (88)
T ss_pred CHHHHHHHHHHhCcCCcEEeEeEEEEeecc---ceeEEEEEEEEcCCcCcHHHHHHHhccCC
Confidence 377889999999999999999999999998 44444666666655566777766665554
No 6
>cd00292 EF1B Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this exchange reaction.
Probab=35.41 E-value=95 Score=27.88 Aligned_cols=55 Identities=22% Similarity=0.300 Sum_probs=41.8
Q ss_pred hhhhHHHHHHHHHhcCeEEcceeEEEEeecCCCCCcceEEEEEeCCCCCHHHHHHHhc
Q 004909 323 TRTRIYTRILSTLRNGILIGDRKFEFLAFSSSQLRESSAWMFASRYGLTAAEIREWMG 380 (724)
Q Consensus 323 ~~~~i~~Rv~~~L~~Gi~I~gR~y~FLafS~SqLR~~s~wFfa~~~~lt~~~Ir~wmG 380 (724)
..+.+.++++.++.+|+.+++-+.+.+||+-.-| .+.+.-++.....+++.+-+.
T Consensus 18 Dl~~l~~~Ik~~~~~gl~~~~~~~epiaFGlk~L---~i~~vv~D~~~~td~lee~i~ 72 (88)
T cd00292 18 DLDELEEKIRAILMDGLLWGKSKLEPIAFGLKAL---QIYCVVEDDEGGTDELEEAIS 72 (88)
T ss_pred CHHHHHHHHHHhCcCCcEEEEEEEEEeeeEeeEE---EEEEEEEeCCcCcHHHHHHHh
Confidence 3788999999999999999999999999984444 455555665556677765543
No 7
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=22.56 E-value=4e+02 Score=22.95 Aligned_cols=59 Identities=17% Similarity=0.111 Sum_probs=34.8
Q ss_pred HHHHHhcCCCCcHHHHHHHHHCCCCCCCchHHHHHHHHHHHHHHHhhccccceeecCceeeeeeeCCCC
Q 004909 549 QEALELMSPGENTNILKELLICGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGCLDETR 617 (724)
Q Consensus 549 ~~~l~~~~~~~~~~~l~~ml~~Gf~p~~epfl~~~L~~~~~~~L~~Lk~K~RI~Vp~s~~L~GV~DetG 617 (724)
.+++.........+++..|...||..++ + -..+-|++|. -.|++..+|.+.|.++++++
T Consensus 11 ~~li~~~~i~sQ~eL~~~L~~~Gi~vTQ-a--------TiSRDLkeL~-~vKv~~~~g~~~Y~l~~~~~ 69 (70)
T PF01316_consen 11 KELISEHEISSQEELVELLEEEGIEVTQ-A--------TISRDLKELG-AVKVPDGNGKYRYVLPEETE 69 (70)
T ss_dssp HHHHHHS---SHHHHHHHHHHTT-T--H-H--------HHHHHHHHHT--EEEECTTSSEEEE-TTSTT
T ss_pred HHHHHHCCcCCHHHHHHHHHHcCCCcch-h--------HHHHHHHHcC-cEEeeCCCCCEEEEecCcCC
Confidence 3455555566677788888999997532 2 2233344453 56778889999999998876
No 8
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=21.20 E-value=7.7e+02 Score=29.32 Aligned_cols=94 Identities=26% Similarity=0.307 Sum_probs=51.5
Q ss_pred ccccHHHHHHHhcCCCChHHHHHHHHHHHHHHH-HHhcCHHHHHHHHH-hcCC---------------CC---cHHHHHH
Q 004909 507 CFLNRQLISLLSTLGIWDEIFEKKQREAVRQLD-AILTDPLKAQEALE-LMSP---------------GE---NTNILKE 566 (724)
Q Consensus 507 ~~LNRQ~I~iLs~lGV~devF~~lq~~~l~~l~-~~l~d~~~a~~~l~-~~~~---------------~~---~~~~l~~ 566 (724)
-.=|+-.|.-|-++|.|.+--. ..|- .=-.|.+.|..+|= .|+. .+ .+.-+..
T Consensus 555 ~t~Nqs~I~qL~~mGfp~~~~~-------rAL~~tgNqDaEsAMNWLFqHMdDPdlndP~~~~~~vPKkDkeVdE~~~~S 627 (749)
T COG5207 555 FTDNQSLIRQLVDMGFPEEDAA-------RALGITGNQDAESAMNWLFQHMDDPDLNDPFVPPPNVPKKDKEVDESKARS 627 (749)
T ss_pred cCchHHHHHHHHHcCCCHHHHH-------HHHhhccCcchHHHHHHHHhhccCcccCCCCCCCCCCCcccccccHHHHHH
Confidence 3468889999999999954321 1111 11135556666552 2210 01 2334778
Q ss_pred HHHCCCCCCCchHHHHHHHHHHHHHHHhhccccceeecCceeeeee-eCCCCCCCCCcE
Q 004909 567 LLICGYKPDAEPFLSMMLQTFRASKLLELRTKTRIFIPNGRSMMGC-LDETRTLNYGQV 624 (724)
Q Consensus 567 ml~~Gf~p~~epfl~~~L~~~~~~~L~~Lk~K~RI~Vp~s~~L~GV-~DetG~L~~gEV 624 (724)
|+..|+.|..+ | +.|.+.....+ +.+.+| -|+.|+..|.||
T Consensus 628 lle~Gln~n~~----------R-kal~~~n~d~~------r~V~w~~N~~D~tF~EP~v 669 (749)
T COG5207 628 LLENGLNPNLC----------R-KALMDMNTDSK------RRVVWCINDDDGTFPEPEV 669 (749)
T ss_pred HHHcCCCHHHH----------H-HHHHHccCCch------heEEEEEeCCCCCCCCCCC
Confidence 99999987422 2 22333322211 233333 489999998876
No 9
>PHA02770 hypothetical protein; Provisional
Probab=18.64 E-value=1.1e+02 Score=26.03 Aligned_cols=19 Identities=32% Similarity=0.744 Sum_probs=14.4
Q ss_pred eEEcceeEEE-EeecCCCCCcceE
Q 004909 339 ILIGDRKFEF-LAFSSSQLRESSA 361 (724)
Q Consensus 339 i~I~gR~y~F-LafS~SqLR~~s~ 361 (724)
+.++||||+| |-|| +++|+
T Consensus 46 lei~~~hyrfelifs----kdnsv 65 (81)
T PHA02770 46 LEVNGRHYRFELIFS----KDNSV 65 (81)
T ss_pred EEEcCceEEEEEEEe----cCCcE
Confidence 5689999998 7777 45554
No 10
>PHA02097 hypothetical protein
Probab=17.00 E-value=1.3e+02 Score=24.52 Aligned_cols=28 Identities=21% Similarity=0.325 Sum_probs=19.1
Q ss_pred eeeecCcEEEeCCeecc--ccCcceeeccc
Q 004909 406 LSVHMDEIEIIPDVKIE--IGKTKYVFSDG 433 (724)
Q Consensus 406 v~v~~~~i~~i~DI~~~--~~g~~~~FTDG 433 (724)
..++.-++..|+||++- .|+++|.|--|
T Consensus 30 f~~~~f~~~fi~~ikvv~~~n~ng~~~~hg 59 (59)
T PHA02097 30 FDVSNFKIQFIAGVKVVKDANYNGFELVHG 59 (59)
T ss_pred EeeccceEEEeCCcEEEecCCCCcEEEecC
Confidence 34455567889999853 46778887654
Done!