Query psy7793
Match_columns 316
No_of_seqs 150 out of 397
Neff 5.6
Searched_HMMs 46136
Date Fri Aug 16 18:59:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7793.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7793hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2140|consensus 100.0 1E-106 2E-111 799.0 19.1 299 13-316 251-630 (739)
2 KOG2141|consensus 100.0 1.1E-31 2.3E-36 273.7 8.9 284 9-300 416-782 (822)
3 KOG2140|consensus 99.2 5E-12 1.1E-16 127.2 1.3 96 10-109 536-638 (739)
4 PF02854 MIF4G: MIF4G domain; 98.4 3.3E-07 7.1E-12 80.0 5.4 92 12-108 98-209 (209)
5 smart00544 MA3 Domain in DAP-5 98.4 4.5E-07 9.8E-12 74.0 5.0 46 201-246 65-113 (113)
6 smart00543 MIF4G Middle domain 98.4 5E-07 1.1E-11 79.1 5.5 92 12-108 91-200 (200)
7 PF02847 MA3: MA3 domain; Int 98.3 1.1E-06 2.4E-11 71.5 5.2 46 201-246 65-113 (113)
8 PF09088 MIF4G_like: MIF4G lik 46.4 1E+02 0.0022 28.2 7.7 79 198-276 98-177 (191)
9 KOG2051|consensus 40.3 32 0.0007 38.8 4.0 83 20-103 525-612 (1128)
10 PF09905 DUF2132: Uncharacteri 33.6 52 0.0011 25.0 3.1 32 266-297 9-46 (64)
11 PF06708 DUF1195: Protein of u 32.3 46 0.00099 29.2 2.9 48 200-247 107-154 (157)
12 KOG0401|consensus 27.0 18 0.00038 40.7 -0.6 86 21-109 480-574 (970)
13 KOG2141|consensus 25.5 1.8E+02 0.0039 31.9 6.5 85 10-100 702-788 (822)
14 PF04494 TFIID_90kDa: WD40 ass 22.4 1.7E+02 0.0036 24.9 4.7 116 151-273 10-139 (142)
15 PF12752 SUZ: SUZ domain; Int 20.1 98 0.0021 22.6 2.4 21 151-171 38-58 (59)
No 1
>KOG2140|consensus
Probab=100.00 E-value=9.8e-107 Score=798.99 Aligned_cols=299 Identities=52% Similarity=0.838 Sum_probs=289.2
Q ss_pred chhhHhHHHHHHHHHhhcCccceeeeeeee----cccCCCCchHHHHHHHH---HHHHHhhhChhhhHHHHHhhchhhhh
Q psy7793 13 VFHKLRNVAKFFAHQLFTDAIGWHVLSCIH----LNEEETTSSGRIFIKIL---FQELSEYMGLSKLNQKIKDPFRPVAR 85 (316)
Q Consensus 13 e~~ql~n~~kFlaHL~n~~~V~~~eililq----LlE~~Td~Svei~i~~L---Gq~L~e~~~~~~l~~~I~erlr~~iL 85 (316)
+--.|-|+++|+|||+||+ | +||+++|| |||.|||+||||||.|| |++|.+++|. |++ +||+|||. ||
T Consensus 251 Dk~~c~~~~kfiahLinq~-V-ahEIv~Leil~lLLe~PTddSvevaI~flkecGakL~~VSpr-~~n-~IfErlR~-IL 325 (739)
T KOG2140|consen 251 DKVSCLNASKFIAHLINQQ-V-AHEIVALEILTLLLERPTDDSVEVAIAFLKECGAKLAEVSPR-ALN-GIFERLRY-IL 325 (739)
T ss_pred chHHHHHHHHHHHHHHHHH-H-HHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHHhChH-HHh-HHHHHHHH-HH
Confidence 3457899999999999999 9 99999999 89999999999999999 9999999999 988 99999999 99
Q ss_pred hhcchhHHHHHHHHHHHHHHhcCCCCCCCccCcCCCCCCCCcceeEeeccCcCCccccCCceeeChhhhhhHHHHHHhhH
Q psy7793 86 WKGKLEKRVQYMIEVLAQVRKDNFKDFPDVIEDLDLVPEEDKFTHLMTLDGVKDTQDILNVFQYDPEYLMNEEKYTTLRR 165 (316)
Q Consensus 86 ~e~~i~~r~q~~IE~Lf~ir~~~fk~~p~v~~eLdLve~~dq~tH~i~ld~~~~~e~~L~~F~~d~~~~~~E~~y~~~k~ 165 (316)
|+|++++|+|||||+||++|+++||++|+++++||||+++||+||.++|+|+++|++.|++|++||+|++||++|++||+
T Consensus 326 he~Eld~rvqy~iEtlf~iRkdkfk~~p~v~~~LDlvee~dq~tH~l~l~de~dpe~~L~vFk~dp~f~ene~kydaikk 405 (739)
T KOG2140|consen 326 HEGELDRRVQYMIETLFQIRKDKFKSHPAVLEELDLVEEEDQITHSLSLEDEDDPEKELGVFKKDPNFEENEEKYDAIKK 405 (739)
T ss_pred hHhhHHHHHHHHHHHHHHHHHHhhccCCccccccCccchhhheeeeeecccccChhhhhcccccCccHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHcCCCCC---C--------hh--------------------HHHHHHhhhhHHHHhhccCChhhh--------------
Q psy7793 166 EILGDEDE---D--------DE--------------------ETNLVALRRTIYLTIHSSLDFEDC-------------- 200 (316)
Q Consensus 166 eilg~~~~---d--------~~--------------------e~~lv~lRr~IYLtimSSld~eEa-------------- 200 (316)
+|||++++ | ++ ++|+|+|||+||||||||+||+||
T Consensus 406 eiLgn~dsen~d~~~~s~E~~~eee~e~~ee~~e~~qI~D~T~~Nlv~frr~IYLti~SSldfeEaaHKLLKmkip~~q~ 485 (739)
T KOG2140|consen 406 EILGNEDSENEDDEDGSSEDDDEEEDESVEEDEEKLQIIDMTETNLVNFRRTIYLTIQSSLDFEEAAHKLLKMKIPESQE 485 (739)
T ss_pred HHhcCCcccccccccccccccccccccccccccccceeeccccchhHHhhhhheeeeeccCcHHHHHHHHHhccCCchhh
Confidence 99997533 1 00 679999999999999999999999
Q ss_pred -----------------------------hhhhhchHHHHHHHHHHHhhhhccchhhHhHHHHHHHHHHhhCCcccchhc
Q psy7793 201 -----------------------------LINKMYVAPLEQIFRESYSTVHRLDINKLRNVAKFFAHQLFTDAIGWHVLS 251 (316)
Q Consensus 201 -----------------------------~~~r~~~~~F~~~F~~~Y~~i~~~e~n~Lrn~akff~hLl~td~l~w~vl~ 251 (316)
.++|.||.+|++||.++|.+|||+|||||||+||||||||+||+|||+||.
T Consensus 486 ~elc~mii~cc~QerTy~kFYglL~eRfc~l~r~~q~~fe~~f~q~YstIhr~EtnkLRnlakffahLlstd~lpw~vl~ 565 (739)
T KOG2140|consen 486 KELCNMIIDCCAQERTYEKFYGLLGERFCMLHREWQEAFEKCFKQQYSTIHRYETNKLRNLAKFFAHLLSTDALPWDVLA 565 (739)
T ss_pred HHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcccccchHHHH
Confidence 889999999999999999999999999999999999999999999999999
Q ss_pred eeEeCcCccCchhHHHHHHHHHHHHHHhChHHHHhhhcCCCchhhhcCCCCCCCCCCceeecccC
Q psy7793 252 CIHLNEEETTSSGRIFIKILFQELSEYMGLSKLNQKIKDPLLAPAMEGVFPRDNPKNTRFAINFF 316 (316)
Q Consensus 252 ~I~ltE~dttss~RIfiK~lfqel~e~lGi~~l~~rl~d~~l~~~~~glFP~d~~~~~rfsINfF 316 (316)
||+|||+|||||||||||||||||||+||+++|++||+||+|||+|+||||+|||+|+|||||||
T Consensus 566 ~ikLTEEdTtsssRIfiKilFqELve~lGl~~L~~RL~dptl~~~l~glFP~dnp~n~RfsINfF 630 (739)
T KOG2140|consen 566 CIKLTEEDTTSSSRIFIKILFQELVEALGLDKLNERLNDPTLQPKLEGLFPRDNPRNTRFSINFF 630 (739)
T ss_pred HhhcccccCCccceehHHHHHHHHHHHhChHHHHHHhcCcchhhhhhccCcCCCcccceeeeehh
Confidence 99999999999999999999999999999999999999999999999999999999999999999
No 2
>KOG2141|consensus
Probab=99.97 E-value=1.1e-31 Score=273.69 Aligned_cols=284 Identities=18% Similarity=0.225 Sum_probs=218.2
Q ss_pred CCCcchhhHhHHHHHHHHHhhcCccceeeeeeee----cccCCCCchHHHHHHHH---HHHHHhhhChhhhHHHHHhhch
Q psy7793 9 LPGLVFHKLRNVAKFFAHQLFTDAIGWHVLSCIH----LNEEETTSSGRIFIKIL---FQELSEYMGLSKLNQKIKDPFR 81 (316)
Q Consensus 9 ~~~~e~~ql~n~~kFlaHL~n~~~V~~~eililq----LlE~~Td~Svei~i~~L---Gq~L~e~~~~~~l~~~I~erlr 81 (316)
..++.+|+|.|++.|+|||||++ | +++.++++ |.+++|.-++++++.++ |+.|+.++|. ++...|-+-..
T Consensus 416 ~~~~~~K~~~Nl~~~l~ylynF~-i-vs~~LiydiI~kl~~~l~e~~ve~ll~ii~~~G~~LRkDDp~-alk~~i~eiq~ 492 (822)
T KOG2141|consen 416 EMDLKDKSLNNIVLFLSYLYNFG-I-VSCSLIYDIIRKLAENLNETNVEALLTIIANCGFSLRKDDPL-ALKDIITEIQS 492 (822)
T ss_pred hcccccchhhhHHHHHHHHHHhh-c-ccHHHHHHHHHHHHhchhhhhHHHHHHHHHHccchhcCCChH-HHHHHHHHHHH
Confidence 45677999999999999999999 7 78888776 88999999999999988 9999999999 89866666555
Q ss_pred hhhhhh--cchhHHHHHHHHHHHHHHhcCCCCCCCccCcCCCCC--------------CCCcceeEeeccCcCCccccCC
Q psy7793 82 PVARWK--GKLEKRVQYMIEVLAQVRKDNFKDFPDVIEDLDLVP--------------EEDKFTHLMTLDGVKDTQDILN 145 (316)
Q Consensus 82 ~~iL~e--~~i~~r~q~~IE~Lf~ir~~~fk~~p~v~~eLdLve--------------~~dq~tH~i~ld~~~~~e~~L~ 145 (316)
. +-.- .-++.|++||+|++.++++|+.++.|..+++. |+ ...+..-.++|+|-+++|....
T Consensus 493 ~-a~~a~~s~~~pR~rFmleti~aLKnN~~kki~~~d~e~--ve~lrk~~k~l~~~~~s~~~~~l~vTledll~ae~kGr 569 (822)
T KOG2141|consen 493 K-AASAKISAISPRLRFMLETISALKNNKLKKIPYADPER--VENLRKLKKALGSSASSSVSLPLSVTLEDLLHAEQKGR 569 (822)
T ss_pred H-hhcCCccccchHHHHHHHHHHHHhcCCCcCCCcCChHH--HHHHHHHHHHHHhccchhhhccccccHHHhhChHhcCc
Confidence 5 3222 23589999999999999999999999887764 32 2224444578888888888888
Q ss_pred ceeeChhhhhhHHHH--------HHhhHhHcCCCCCCh-h----HHHHHHhhhhHHHHhhccCChhhh------------
Q psy7793 146 VFQYDPEYLMNEEKY--------TTLRREILGDEDEDD-E----ETNLVALRRTIYLTIHSSLDFEDC------------ 200 (316)
Q Consensus 146 ~F~~d~~~~~~E~~y--------~~~k~eilg~~~~d~-~----e~~lv~lRr~IYLtimSSld~eEa------------ 200 (316)
||.++..|-.+++-- ....+.--|...++- + +.+++++||.|||+||||.||.+|
T Consensus 570 WWlVGsaw~g~~~~~~s~~~~~d~~~~k~~~gs~~~kmL~lArkqrMNTdiRr~IFcsImsaeDyiDAFEklLkL~LK~~ 649 (822)
T KOG2141|consen 570 WWLVGSAWRGNEQFMGSINTASDSAKSKKAEGSFADKMLELARKQRMNTDIRRAIFCSIMSAEDYIDAFEKLLKLSLKGK 649 (822)
T ss_pred eEEecchhcCCcccccccchHhHHhhhhcccCCccHHHHHHHHHhhcchHhhhhheeeeecchHHHHHHHHHHhccCCCc
Confidence 888888777755411 111111111111110 0 789999999999999999999999
Q ss_pred -------------------------------hhhhhchHHHHHHHHHHHhhhhccchhhHhHHHHHHHHHHhhCCcccch
Q psy7793 201 -------------------------------LINKMYVAPLEQIFRESYSTVHRLDINKLRNVAKFFAHQLFTDAIGWHV 249 (316)
Q Consensus 201 -------------------------------~~~r~~~~~F~~~F~~~Y~~i~~~e~n~Lrn~akff~hLl~td~l~w~v 249 (316)
..++.++.+||.|+|+.+..++.+.+-+++|+|+|+|||++++++|++|
T Consensus 650 Q~rEI~~VllhC~l~EK~yNpfYa~lA~KfCe~~~~~~~tfQF~~WD~f~ele~ls~~ri~nLa~l~a~Li~~~~lsLtV 729 (822)
T KOG2141|consen 650 QEREIARVLLHCCLNEKTYNPFYALLALKFCEFNKNLKKTFQFALWDRFKELEQLSLFRISNLAKLLASLISNAVLSLTV 729 (822)
T ss_pred chHHHHHHHHHHHhhhcccchHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhhhcchhhHhHHHHHHHHHHHhcccceee
Confidence 7899999999999999999999999999999999999999999999999
Q ss_pred hceeEeCcCccCchhHHHHHHHHHHHHHH---hChHHHHhhh-cCCCchhhhcCC
Q psy7793 250 LSCIHLNEEETTSSGRIFIKILFQELSEY---MGLSKLNQKI-KDPLLAPAMEGV 300 (316)
Q Consensus 250 l~~I~ltE~dttss~RIfiK~lfqel~e~---lGi~~l~~rl-~d~~l~~~~~gl 300 (316)
|+.|.+.+.++ .+--|+|.+|-.|.-. =-+-.+..|. +.|.++-..+|+
T Consensus 730 LK~Vdfm~l~~--~~~~fl~~~l~~l~l~~~~~~v~~~ftr~~kn~k~~~l~~gv 782 (822)
T KOG2141|consen 730 LKHVDFMELNA--RRTTFLKKLLFGLILEPEEKDVFQLFTRVAKNTKLELLSEGV 782 (822)
T ss_pred eeeccHhhcCh--HHHHHHHHHHHHHHhcchHHHHHHHHHHHhcCHHHHHHHHHH
Confidence 99999995544 4445666555554332 1233445555 455565555553
No 3
>KOG2140|consensus
Probab=99.18 E-value=5e-12 Score=127.20 Aligned_cols=96 Identities=44% Similarity=0.677 Sum_probs=83.9
Q ss_pred CCcchhhHhHHHHHHHHHhhcCccceeeeeeeecccCCCCchHHHHHHHHHHHHHhhhChhhhHHHHHhhchhhhhh---
Q psy7793 10 PGLVFHKLRNVAKFFAHQLFTDAIGWHVLSCIHLNEEETTSSGRIFIKILFQELSEYMGLSKLNQKIKDPFRPVARW--- 86 (316)
Q Consensus 10 ~~~e~~ql~n~~kFlaHL~n~~~V~~~eililqLlE~~Td~Svei~i~~LGq~L~e~~~~~~l~~~I~erlr~~iL~--- 86 (316)
+..|+++|||+++|||||+.++++||+++.++.|+|+.|++|.||+|+||||+|++..|.. .+-+||.+.-||
T Consensus 536 hr~EtnkLRnlakffahLlstd~lpw~vl~~ikLTEEdTtsssRIfiKilFqELve~lGl~----~L~~RL~dptl~~~l 611 (739)
T KOG2140|consen 536 HRYETNKLRNLAKFFAHLLSTDALPWDVLACIKLTEEDTTSSSRIFIKILFQELVEALGLD----KLNERLNDPTLQPKL 611 (739)
T ss_pred HHHhHHHHHHHHHHHHHHhcccccchHHHHHhhcccccCCccceehHHHHHHHHHHHhChH----HHHHHhcCcchhhhh
Confidence 6799999999999999999999999999999999999999999999999999999998874 555666663333
Q ss_pred ----hcchhHHHHHHHHHHHHHHhcCC
Q psy7793 87 ----KGKLEKRVQYMIEVLAQVRKDNF 109 (316)
Q Consensus 87 ----e~~i~~r~q~~IE~Lf~ir~~~f 109 (316)
+.+..+.++|.|+.+..|..++.
T Consensus 612 ~glFP~dnp~n~RfsINfFTsIGLGgL 638 (739)
T KOG2140|consen 612 EGLFPRDNPRNTRFSINFFTSIGLGGL 638 (739)
T ss_pred hccCcCCCcccceeeeehhhhhccccc
Confidence 34677889999999999988776
No 4
>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=98.42 E-value=3.3e-07 Score=79.97 Aligned_cols=92 Identities=17% Similarity=0.204 Sum_probs=76.8
Q ss_pred cchhhHhHHHHHHHHHhhcCccceeeeeeee----cccCCCC--------chHHHHHHHH---HHHHH--hhhChhhhHH
Q psy7793 12 LVFHKLRNVAKFFAHQLFTDAIGWHVLSCIH----LNEEETT--------SSGRIFIKIL---FQELS--EYMGLSKLNQ 74 (316)
Q Consensus 12 ~e~~ql~n~~kFlaHL~n~~~V~~~eililq----LlE~~Td--------~Svei~i~~L---Gq~L~--e~~~~~~l~~ 74 (316)
...++..+.++|+|+||+++ | +++-.+++ |+...++ .++++++.+| |..|. ...+. .++
T Consensus 98 ~~~~~~~~~~~fl~eL~~~~-v-v~~~~i~~~l~~ll~~~~~~~~~~~~~~~ie~~~~lL~~~G~~l~~~~~~~~-~l~- 173 (209)
T PF02854_consen 98 SSKQRRRGNIRFLAELFNFG-V-VSEKIIFDILRELLSDGTDECQPPPDEENIECLCTLLKTCGKKLENSEESPK-ALD- 173 (209)
T ss_dssp HHHHHHHHHHHHHHHHHHTT-S-SCHHHHHHHHHHHHHHTSHHCCHHTCHHHHHHHHHHHHHHHHHHHHCHHHHH-HHH-
T ss_pred HHHHHHhhhhhHHHhhHhhc-c-ccchhHHHHHHHHHhcccccccCCCcHhHHHHHHHHHHHHHHHHhcCCCchh-HHH-
Confidence 34567899999999999999 6 56555544 6666555 8999999999 99999 88777 677
Q ss_pred HHHhhchhhhhhh---cchhHHHHHHHHHHHHHHhcC
Q psy7793 75 KIKDPFRPVARWK---GKLEKRVQYMIEVLAQVRKDN 108 (316)
Q Consensus 75 ~I~erlr~~iL~e---~~i~~r~q~~IE~Lf~ir~~~ 108 (316)
.++++++. .... +.++.|+++|++.++++|+++
T Consensus 174 ~~~~~~~~-~~~~~~~~~~~~r~~~~l~~l~~lr~~~ 209 (209)
T PF02854_consen 174 EIFERLQK-YANSKKDPNLSSRIRFMLEDLIELRNNK 209 (209)
T ss_dssp HHHHHHHH-HHHHCHSSSSSHHHHHHHHHHHHHHHTC
T ss_pred HHHHHHHH-HHHhhcccCCCHHHHHHHHHHHHHhcCC
Confidence 99999999 6665 899999999999999999985
No 5
>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=98.38 E-value=4.5e-07 Score=74.00 Aligned_cols=46 Identities=22% Similarity=0.324 Sum_probs=43.2
Q ss_pred hhhhhchHHHHHHHHHHHhhhhccch---hhHhHHHHHHHHHHhhCCcc
Q psy7793 201 LINKMYVAPLEQIFRESYSTVHRLDI---NKLRNVAKFFAHQLFTDAIG 246 (316)
Q Consensus 201 ~~~r~~~~~F~~~F~~~Y~~i~~~e~---n~Lrn~akff~hLl~td~l~ 246 (316)
+.+..++..|+++||+.|+.+++++. +...|+|+|+|++++.|.+|
T Consensus 65 ~~~~~~~~~~~~~f~~~~~~l~dl~~D~P~a~~~la~~~a~~v~~~~l~ 113 (113)
T smart00544 65 QANVISTKQFEKGFWRLLEDIEDLELDIPNAWRNLAEFVARLISDGILP 113 (113)
T ss_pred HcCCcCHHHHHHHHHHHHhhChhhhcccccHHHHHHHHHHHHHHcCCCC
Confidence 56788999999999999999999998 89999999999999999987
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=98.38 E-value=5e-07 Score=79.10 Aligned_cols=92 Identities=18% Similarity=0.248 Sum_probs=76.6
Q ss_pred cchhhHhHHHHHHHHHhhcCccceeeeeeee----cccCCCC-------chHHHHHHHH---HHHHH-hhhChhhhHHHH
Q psy7793 12 LVFHKLRNVAKFFAHQLFTDAIGWHVLSCIH----LNEEETT-------SSGRIFIKIL---FQELS-EYMGLSKLNQKI 76 (316)
Q Consensus 12 ~e~~ql~n~~kFlaHL~n~~~V~~~eililq----LlE~~Td-------~Svei~i~~L---Gq~L~-e~~~~~~l~~~I 76 (316)
..-++.++.++|+|+|++++ | ++.-.+++ |++.++. .++++++.+| |+.|. ...|. .++ .+
T Consensus 91 ~~~~~~~~~i~fl~eL~~~~-~-i~~~~i~~~l~~ll~~~~~~~~~~~~~~ve~l~~lL~~~G~~l~~~~~~~-~~~-~~ 166 (200)
T smart00543 91 SDKQRRLGLVRFLGELYNFQ-V-LTSKIILELLKELLNDLTKLDPPRSDFSVECLLSLLPTCGKDLEREKSPK-LLD-EI 166 (200)
T ss_pred HhhhhHHhHHHHHHHHHHcc-c-CcHHHHHHHHHHHHhccCCCCCCCcHHHHHHHHHHHHHhhHHHcCcccHH-HHH-HH
Confidence 45578899999999999999 6 55555554 6666665 7999999999 99999 77777 777 99
Q ss_pred Hhhchhhhhhhc---chhHHHHHHHHHHHHHHhcC
Q psy7793 77 KDPFRPVARWKG---KLEKRVQYMIEVLAQVRKDN 108 (316)
Q Consensus 77 ~erlr~~iL~e~---~i~~r~q~~IE~Lf~ir~~~ 108 (316)
+++++. ....+ ..+.|++||++.+.++|++.
T Consensus 167 l~~l~~-~~~~~~~~~~~~r~~~~l~~l~~l~~~~ 200 (200)
T smart00543 167 LERLQD-YLLKKDKTELSSRLRFMLELLIELRKNK 200 (200)
T ss_pred HHHHHH-HHhcccccCCChHHHHHHHHHHHHhhCc
Confidence 999999 66665 79999999999999999863
No 7
>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=98.28 E-value=1.1e-06 Score=71.53 Aligned_cols=46 Identities=13% Similarity=0.235 Sum_probs=41.7
Q ss_pred hhhhhchHHHHHHHHHHHhhhhccchh---hHhHHHHHHHHHHhhCCcc
Q psy7793 201 LINKMYVAPLEQIFRESYSTVHRLDIN---KLRNVAKFFAHQLFTDAIG 246 (316)
Q Consensus 201 ~~~r~~~~~F~~~F~~~Y~~i~~~e~n---~Lrn~akff~hLl~td~l~ 246 (316)
..+...+..|+++|++.++.+++++.. ..+|+|+|+||+++.|+||
T Consensus 65 ~~~~~~~~~~~~gf~~~l~~l~Dl~~D~P~~~~~la~~~~~~i~~~~lp 113 (113)
T PF02847_consen 65 KRKLISKEQFQEGFEDLLESLEDLELDIPKAPEYLAKFLARLIADGILP 113 (113)
T ss_dssp HTTSS-HHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTSS-
T ss_pred hcCCCCHHHHHHHHHHHHhHhhhccccchHHHHHHHHHHHHHHHcCCcC
Confidence 567888999999999999999999988 9999999999999999997
No 8
>PF09088 MIF4G_like: MIF4G like; InterPro: IPR015172 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 1", and is found in nuclear cap-binding proteins and eIF4G. 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.; GO: 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A.
Probab=46.40 E-value=1e+02 Score=28.16 Aligned_cols=79 Identities=18% Similarity=0.285 Sum_probs=59.0
Q ss_pred hhhhhh-hhchHHHHHHHHHHHhhhhccchhhHhHHHHHHHHHHhhCCcccchhceeEeCcCccCchhHHHHHHHHHHHH
Q psy7793 198 EDCLIN-KMYVAPLEQIFRESYSTVHRLDINKLRNVAKFFAHQLFTDAIGWHVLSCIHLNEEETTSSGRIFIKILFQELS 276 (316)
Q Consensus 198 eEa~~~-r~~~~~F~~~F~~~Y~~i~~~e~n~Lrn~akff~hLl~td~l~w~vl~~I~ltE~dttss~RIfiK~lfqel~ 276 (316)
|=|+.. ......|.++.+.-|+.+++++..-.+..+-.|+|=|+.=.-.|.==+.+.-.+.+...+.|+|++-++...+
T Consensus 98 elCk~~P~~i~pv~~~air~ly~~l~~md~e~~~Rf~dWfS~hLSNF~f~W~W~eW~~~~~l~~~~pk~~Fi~~~l~k~i 177 (191)
T PF09088_consen 98 ELCKLSPSAIPPVLGRAIRFLYRNLDSMDFELRDRFVDWFSHHLSNFGFQWKWDEWVDDLELPPLHPKRVFIREVLEKEI 177 (191)
T ss_dssp HHHHHSTTTHHHHHHHHHHHHHHGGGGB-HHHHHHHHHHHHHHHHTTTT---GGGGGGGTTS-TTSHHHHHHHHHHHHHH
T ss_pred HHHHhCHHHHHHHHHHHHHHHHHhhhhcCHHHHHHHHHHHHHHHhcCCceeeHHHhhhhhhCCccCCHHHHHHHHHHHHH
Confidence 446444 6788999999999999999999999999999999999876665532133333466667899999999887654
No 9
>KOG2051|consensus
Probab=40.32 E-value=32 Score=38.80 Aligned_cols=83 Identities=13% Similarity=0.093 Sum_probs=54.3
Q ss_pred HHHHHHHHhhcCccceee-eeeee-cccCCCCchHHHHHHHH---HHHHHhhhChhhhHHHHHhhchhhhhhhcchhHHH
Q psy7793 20 VAKFFAHQLFTDAIGWHV-LSCIH-LNEEETTSSGRIFIKIL---FQELSEYMGLSKLNQKIKDPFRPVARWKGKLEKRV 94 (316)
Q Consensus 20 ~~kFlaHL~n~~~V~~~e-ililq-LlE~~Td~Svei~i~~L---Gq~L~e~~~~~~l~~~I~erlr~~iL~e~~i~~r~ 94 (316)
+++|||.|+-++.||.++ +.++. |+-..|..+||+++.+| |.+|-..--.........++++. .=.....+.|-
T Consensus 525 ~VrfIsEL~KF~lv~~~~if~cLk~ll~dF~~hnIEm~c~lLE~~GrfLlr~pEt~lrM~~~Le~i~r-kK~a~~lDsr~ 603 (1128)
T KOG2051|consen 525 IVRFISELCKFQLVPKFEIFSCLKMLLNDFTHHNIEMACVLLESCGRFLLRSPETKLRMRVFLEQIKR-KKRASALDSRQ 603 (1128)
T ss_pred hhhhHHhhhhhCccChHHHHHHHHHHHHhcccccHHHHHHHHHhcchhhhcChhHHHHHHHHHHHHHH-HHHHhhhchHH
Confidence 468999999999554443 33455 88889999999999999 99986653331111233444443 33345667777
Q ss_pred HHHHHHHHH
Q psy7793 95 QYMIEVLAQ 103 (316)
Q Consensus 95 q~~IE~Lf~ 103 (316)
+-+||...-
T Consensus 604 ~~~iENay~ 612 (1128)
T KOG2051|consen 604 ATLIENAYY 612 (1128)
T ss_pred HHHHHHhHH
Confidence 777776444
No 10
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=33.60 E-value=52 Score=24.99 Aligned_cols=32 Identities=22% Similarity=0.544 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHhChHHHHhhh------cCCCchhhh
Q psy7793 266 IFIKILFQELSEYMGLSKLNQKI------KDPLLAPAM 297 (316)
Q Consensus 266 IfiK~lfqel~e~lGi~~l~~rl------~d~~l~~~~ 297 (316)
|=++-+..+|+++.|-+.|-+|+ +||+++.++
T Consensus 9 vtLe~il~~Lv~~yGW~~L~~~i~i~CF~~~PsikSSL 46 (64)
T PF09905_consen 9 VTLETILTELVEHYGWEELGERININCFKNNPSIKSSL 46 (64)
T ss_dssp --HHHHHHHHHHHT-HHHHHHHTTSSSTTSS--HHHHH
T ss_pred hhHHHHHHHHHHHhCHHHHHhhcccccCCCCCchHHHH
Confidence 44678899999999999999998 488887765
No 11
>PF06708 DUF1195: Protein of unknown function (DUF1195); InterPro: IPR010608 This family consists of several plant specific hypothetical proteins of around 160 residues in length. The function of this family is unknown.
Probab=32.25 E-value=46 Score=29.16 Aligned_cols=48 Identities=15% Similarity=0.183 Sum_probs=40.4
Q ss_pred hhhhhhchHHHHHHHHHHHhhhhccchhhHhHHHHHHHHHHhhCCccc
Q psy7793 200 CLINKMYVAPLEQIFRESYSTVHRLDINKLRNVAKFFAHQLFTDAIGW 247 (316)
Q Consensus 200 a~~~r~~~~~F~~~F~~~Y~~i~~~e~n~Lrn~akff~hLl~td~l~w 247 (316)
..+-|-||++|+.+..+--...-.-.-..+.-+||...|-+--|..|-
T Consensus 107 vrLPrFWqEAFeAAYe~L~sD~~~VrdaAisEIAkmS~r~~~~~~~~~ 154 (157)
T PF06708_consen 107 VRLPRFWQEAFEAAYEELASDVPQVRDAAISEIAKMSVRSIELDPPPN 154 (157)
T ss_pred ccCchHHHHHHHHHHHHHhccCcchhHHHHHHHHHHhhccccCCCCCC
Confidence 467899999999998888777777788889999999999887776664
No 12
>KOG0401|consensus
Probab=26.98 E-value=18 Score=40.69 Aligned_cols=86 Identities=13% Similarity=0.241 Sum_probs=59.4
Q ss_pred HHHHHHHhhcCccceeeee---eee-cccC--CCCchHHHHHHHH---HHHHHhhhChhhhHHHHHhhchhhhhhhcchh
Q psy7793 21 AKFFAHQLFTDAIGWHVLS---CIH-LNEE--ETTSSGRIFIKIL---FQELSEYMGLSKLNQKIKDPFRPVARWKGKLE 91 (316)
Q Consensus 21 ~kFlaHL~n~~~V~~~eil---ilq-LlE~--~Td~Svei~i~~L---Gq~L~e~~~~~~l~~~I~erlr~~iL~e~~i~ 91 (316)
.+|++-|+-.+ + |.+-+ |++ |+.. +.+.++++.+.|+ |..+....+........|.+... +.-....+
T Consensus 480 ~~~ig~l~~~~-m-l~e~i~~~~v~~Ll~~~~~~ee~ie~lc~f~~tig~~lD~~~~s~r~md~~~~~~k~-~~~~~~~s 556 (970)
T KOG0401|consen 480 FRFIGELFKLK-M-LTEKIVHACVQKLLSDDQPSEESIECLCRFLTTIGKKLDFSKESPRNMDEYFNSMKN-LKRKPQRS 556 (970)
T ss_pred HHHHHHHHHHH-H-HHHHHHHHHHHHhhccccccchhhhhHHhhhhcccccccccCcccchhHHHHHHHHH-hhhhhhhc
Confidence 36777777776 5 43222 233 6666 5689999999999 65554332221112366777777 66667899
Q ss_pred HHHHHHHHHHHHHHhcCC
Q psy7793 92 KRVQYMIEVLAQVRKDNF 109 (316)
Q Consensus 92 ~r~q~~IE~Lf~ir~~~f 109 (316)
.|++||+..+.++|.++.
T Consensus 557 ~r~RfM~~~~idlR~~~w 574 (970)
T KOG0401|consen 557 NRIRFMLQSVIDLRKSGW 574 (970)
T ss_pred cchhhhhccccccccccc
Confidence 999999999999998887
No 13
>KOG2141|consensus
Probab=25.48 E-value=1.8e+02 Score=31.94 Aligned_cols=85 Identities=20% Similarity=0.287 Sum_probs=47.1
Q ss_pred CCcchhhHhHHHHHHHHHhhcCccceeeeeeeecccCCCCchHHHHHHHHHHHHHhhhChhhhHHHHHhhchhhhhh--h
Q psy7793 10 PGLVFHKLRNVAKFFAHQLFTDAIGWHVLSCIHLNEEETTSSGRIFIKILFQELSEYMGLSKLNQKIKDPFRPVARW--K 87 (316)
Q Consensus 10 ~~~e~~ql~n~~kFlaHL~n~~~V~~~eililqLlE~~Td~Svei~i~~LGq~L~e~~~~~~l~~~I~erlr~~iL~--e 87 (316)
..+-.-++.|.++|+|||+...+.+...+-.++++ ..+...+...-++++.-+.+. ..+ .+++.+..+... .
T Consensus 702 e~ls~~ri~nLa~l~a~Li~~~~lsLtVLK~Vdfm-~l~~~~~~fl~~~l~~l~l~~----~~~-~v~~~ftr~~kn~k~ 775 (822)
T KOG2141|consen 702 EQLSLFRISNLAKLLASLISNAVLSLTVLKHVDFM-ELNARRTTFLKKLLFGLILEP----EEK-DVFQLFTRVAKNTKL 775 (822)
T ss_pred hhcchhhHhHHHHHHHHHHHhcccceeeeeeccHh-hcChHHHHHHHHHHHHHHhcc----hHH-HHHHHHHHHhcCHHH
Confidence 34566789999999999998884544455455555 334444544444554433222 123 555555541111 2
Q ss_pred cchhHHHHHHHHH
Q psy7793 88 GKLEKRVQYMIEV 100 (316)
Q Consensus 88 ~~i~~r~q~~IE~ 100 (316)
+.++.-++.-|..
T Consensus 776 ~~l~~gvk~F~~~ 788 (822)
T KOG2141|consen 776 ELLSEGVKWFLKH 788 (822)
T ss_pred HHHHHHHHHHHHH
Confidence 3455555555554
No 14
>PF04494 TFIID_90kDa: WD40 associated region in TFIID subunit; InterPro: IPR007582 This region, possibly a domain is found in subunits of transcription factor TFIID. The function of this region is unknown.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2J4B_D 2J49_A 2NXP_F.
Probab=22.39 E-value=1.7e+02 Score=24.93 Aligned_cols=116 Identities=17% Similarity=0.214 Sum_probs=58.4
Q ss_pred hhhhhhHHHHHHhhHhHcCCCCCChhHHHHHHhhh-------hHHHHhhccCChhhh-hhhhhchHHHHHHHHHHHhhhh
Q psy7793 151 PEYLMNEEKYTTLRREILGDEDEDDEETNLVALRR-------TIYLTIHSSLDFEDC-LINKMYVAPLEQIFRESYSTVH 222 (316)
Q Consensus 151 ~~~~~~E~~y~~~k~eilg~~~~d~~e~~lv~lRr-------~IYLtimSSld~eEa-~~~r~~~~~F~~~F~~~Y~~i~ 222 (316)
.+...-++.|..+|.|+.+.- +.---++++ ..||-++++-..++| ..-.+|...|...+.+.-+.+.
T Consensus 10 ~~p~~y~~~y~~l~~wv~~sl-----d~yK~EL~~lLyPvFvh~YL~Lv~~~~~~~A~~F~~kf~~~~~~~~~~~i~~L~ 84 (142)
T PF04494_consen 10 NDPDKYEQAYSRLRNWVDNSL-----DIYKPELSRLLYPVFVHSYLDLVSKGHPEEAKSFLEKFSPDFEDSHQEDIEKLS 84 (142)
T ss_dssp --GCCHHHHHHHHHHHHHTS------HHHHHHHGGGHHHHHHHHHHHHHHTT-HHHHHHHHHHHGGGGHGHGHHHHHHHT
T ss_pred CCHHHHHHHHHHHHHHHHhCc-----HhhHHHHHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 355677899999999997641 122234544 357888888888888 4445555555555444322222
Q ss_pred ccc-hhhHhHHHHHHHHHHhhCCcccc----hhc-eeEeCcCccCchhHHHHHHHHH
Q psy7793 223 RLD-INKLRNVAKFFAHQLFTDAIGWH----VLS-CIHLNEEETTSSGRIFIKILFQ 273 (316)
Q Consensus 223 ~~e-~n~Lrn~akff~hLl~td~l~w~----vl~-~I~ltE~dttss~RIfiK~lfq 273 (316)
.+. +.++ -..-.++++.++..... .+. .+.+-++...+.|+++++||-+
T Consensus 85 ~i~~~~~l--~~~~~~~~~r~~Ky~I~ls~~s~~lL~~fL~~~~~~g~~~ll~iin~ 139 (142)
T PF04494_consen 85 SITSPEHL--EENELARLFRSNKYVIRLSRDSFSLLLQFLQENENSGGSVLLRIINQ 139 (142)
T ss_dssp T--SHHHH--HHSHHHHHHHCSGEEEEEEHHHHHHHHHHHHHTTCHTHHHHHHHHHH
T ss_pred hhCcHHHH--hccHHHHHHHhCCeeEEECHHHHHHHHHHHHhCCcchHHHHHHHHHH
Confidence 211 1222 12345566666533221 111 1112233445556666666544
No 15
>PF12752 SUZ: SUZ domain; InterPro: IPR024771 The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched in positively charged amino acids. It was first characterised in the Caenorhabditis elegans protein SZY-20 where it has been shown to bind RNA and allow their localization to the centrosome [].
Probab=20.15 E-value=98 Score=22.62 Aligned_cols=21 Identities=24% Similarity=0.395 Sum_probs=18.8
Q ss_pred hhhhhhHHHHHHhhHhHcCCC
Q psy7793 151 PEYLMNEEKYTTLRREILGDE 171 (316)
Q Consensus 151 ~~~~~~E~~y~~~k~eilg~~ 171 (316)
..+++=|+.|.+.|..|.|++
T Consensus 38 kSlEERE~eY~~AR~RIFg~~ 58 (59)
T PF12752_consen 38 KSLEEREAEYAEARARIFGSS 58 (59)
T ss_pred CCHHHHHHHHHHHHHHHhCCC
Confidence 468999999999999999974
Done!