Query psy7791
Match_columns 551
No_of_seqs 140 out of 577
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 18:56:27 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7791.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7791hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2140|consensus 100.0 6E-125 1E-129 981.3 32.3 479 19-551 126-605 (739)
2 KOG2141|consensus 100.0 1.4E-94 3E-99 776.5 25.2 455 10-538 279-756 (822)
3 PF02854 MIF4G: MIF4G domain; 99.9 1.6E-25 3.5E-30 215.0 15.7 183 59-253 2-209 (209)
4 smart00543 MIF4G Middle domain 99.9 4E-25 8.6E-30 212.3 17.2 183 59-253 2-200 (200)
5 smart00544 MA3 Domain in DAP-5 99.7 1.1E-18 2.4E-23 154.7 5.6 109 358-506 1-113 (113)
6 PF02847 MA3: MA3 domain; Int 99.7 5.7E-17 1.2E-21 143.5 3.9 109 358-506 1-113 (113)
7 KOG0401|consensus 99.4 5.8E-13 1.3E-17 156.2 9.7 220 23-255 318-575 (970)
8 KOG2051|consensus 99.2 1.4E-10 2.9E-15 132.1 14.3 180 62-251 432-615 (1128)
9 KOG1104|consensus 98.2 6.3E-05 1.4E-09 84.5 17.1 192 52-256 22-246 (759)
10 KOG2051|consensus 97.9 0.00027 5.8E-09 82.0 16.9 140 57-196 630-789 (1128)
11 PF02854 MIF4G: MIF4G domain; 95.2 0.016 3.4E-07 55.3 3.5 106 367-508 11-122 (209)
12 smart00543 MIF4G Middle domain 93.7 0.057 1.2E-06 51.5 3.3 107 369-514 13-122 (200)
13 KOG2412|consensus 92.6 3.9 8.4E-05 45.5 15.5 189 53-247 334-579 (591)
14 KOG3942|consensus 91.6 0.65 1.4E-05 48.1 7.8 122 122-255 199-334 (348)
15 PF09088 MIF4G_like: MIF4G lik 88.8 3.2 7E-05 40.6 9.7 88 415-537 90-178 (191)
16 PF07817 GLE1: GLE1-like prote 82.9 7.4 0.00016 39.7 9.4 83 51-134 23-132 (256)
17 PF02847 MA3: MA3 domain; Int 71.2 18 0.0004 31.4 7.3 104 58-165 2-113 (113)
18 smart00544 MA3 Domain in DAP-5 63.1 61 0.0013 28.1 9.0 104 58-165 2-113 (113)
19 PF15359 CDV3: Carnitine defic 62.1 4.8 0.0001 36.9 1.8 18 20-37 81-98 (129)
20 cd03567 VHS_GGA VHS domain fam 60.6 55 0.0012 30.4 8.5 99 148-260 18-124 (139)
21 cd03568 VHS_STAM VHS domain fa 52.3 1.1E+02 0.0023 28.6 9.0 95 149-258 18-116 (144)
22 PF09733 VEFS-Box: VEFS-Box of 52.2 30 0.00065 32.2 5.3 31 146-176 110-140 (140)
23 cd03569 VHS_Hrs_Vps27p VHS dom 49.2 1.4E+02 0.003 27.7 9.3 96 148-258 21-120 (142)
24 KOG2297|consensus 49.1 51 0.0011 34.9 6.8 60 489-548 147-206 (412)
25 KOG2140|consensus 48.4 90 0.002 35.3 8.9 110 54-174 451-568 (739)
26 cd03561 VHS VHS domain family; 44.6 1.7E+02 0.0037 26.5 9.1 94 149-256 18-116 (133)
27 smart00288 VHS Domain present 44.2 1.9E+02 0.0041 26.3 9.3 71 148-232 17-91 (133)
28 KOG2188|consensus 37.8 2.4E+02 0.0052 32.5 10.3 25 152-176 486-510 (650)
29 TIGR03209 P21_Cbot clostridium 36.3 49 0.0011 29.7 4.1 38 410-449 2-39 (142)
30 PF01602 Adaptin_N: Adaptin N 35.9 3.5E+02 0.0075 29.7 11.5 173 59-246 323-522 (526)
31 PF00790 VHS: VHS domain; Int 30.1 1.7E+02 0.0036 26.8 6.6 95 150-258 24-124 (140)
32 PRK08307 stage III sporulation 30.0 72 0.0016 30.5 4.3 37 410-446 64-101 (171)
33 KOG3117|consensus 29.0 30 0.00066 35.9 1.5 12 23-34 188-199 (340)
34 KOG2229|consensus 28.0 6.6E+02 0.014 28.6 11.5 70 362-453 224-293 (616)
35 TIGR02833 spore_III_AB stage I 27.6 62 0.0013 31.0 3.3 37 410-446 63-100 (170)
36 KOG0122|consensus 25.6 36 0.00079 34.6 1.4 14 22-36 160-173 (270)
37 KOG1060|consensus 25.1 9.4E+02 0.02 28.9 12.4 71 166-246 499-569 (968)
38 KOG0482|consensus 24.1 5E+02 0.011 29.7 9.7 75 163-244 601-684 (721)
39 PF00619 CARD: Caspase recruit 21.9 4.3E+02 0.0093 21.3 7.5 73 54-134 1-73 (85)
No 1
>KOG2140|consensus
Probab=100.00 E-value=6.4e-125 Score=981.35 Aligned_cols=479 Identities=59% Similarity=0.935 Sum_probs=458.6
Q ss_pred ccCCCCCCcccChHHhhhhhhhcCCcchhHHHHhhHHHHHHHHhHHhhhcCCCcHHHHHHHHHHHHhhhhhhHHHHHHHH
Q psy7791 19 ILSSKTGGAYIPPAKLKLMQQSISDKSSVEYQRISWETLKKSIHGSVNKVNTGNIGIIARKLFQENIIRGRGLLTRTILQ 98 (551)
Q Consensus 19 ~~~~~~~~kYVPP~~~r~~~~~~~d~~see~Q~~~w~~L~r~I~glLNKLs~~Ni~~i~~eL~~~n~~~gr~ll~~~Il~ 98 (551)
.+.++++|+||||+++|+|+++.+|+.|.+|||.+|++|+++|+|++|||+.+||..|+.|||+.|+.+|||++|++||+
T Consensus 126 l~~trtGG~YIPPaKL~~mq~qi~Dk~s~~yQRmnWEalkksInglInkvn~sNi~~ii~eLfqeNiirgRgl~crsv~~ 205 (739)
T KOG2140|consen 126 LLRTRTGGAYIPPAKLRMMQAQITDKNSIEYQRMNWEALKKSINGLINKVNASNIQEIIRELFQENIIRGRGLLCRSVMQ 205 (739)
T ss_pred HhhccCCCeecCHHHHHHHHHHhcccchHHHHHHHHHHHHHHhHHHHhhhhHHHHHHHHHHHHHHHHHhccchhHHHHHH
Confidence 45679999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhcCCchHHHHHHHHHHHHccCCchHHHHHHHHHHHHHHHHhccCccchhhHHHHHHHHHhcccccHHHHHHHHHHHhc
Q psy7791 99 AQAASPTFTNVYAALVDIINSKFPSIGELLLNRCIQQFKRSFKRNDKALCINSVTFIAHLVNQQVAHEIIVLEILTLLVE 178 (551)
Q Consensus 99 ~~~~~~~~~~vyAaLia~L~~~~pevG~~ll~~lv~~F~~~~~~~d~k~~~n~~~fia~Lynf~Vv~~~li~dii~~Lle 178 (551)
+|.++|.|+++||||+|+||+++|+||++|+.+++.+|.++|++||+-.|.|.+.|||||+|++|+|++++++|+.+||+
T Consensus 206 aq~asp~ft~vyaALvAviNskfP~IgElLlkrLilqf~r~f~RnDk~~c~~~~kfiahLinq~VahEIv~Leil~lLLe 285 (739)
T KOG2140|consen 206 AQAASPGFTPVYAALVAVINSKFPQIGELLLKRLILQFKRSFRRNDKVSCLNASKFIAHLINQQVAHEIVALEILTLLLE 285 (739)
T ss_pred HHhcCCCCcHHHHHHHHHHccCCchHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcHHHHHHHHHHhhhhhhcccCccccchhhhcchHHHHHHHHHHHhhhcCCCchhHHHHHHHHHHHHHHcCCcCCC
Q psy7791 179 TPTNDSDFSLEPYSKHKLHHLRSLMCMPLWWISSIQSFQALESFFSTDVYNSSKGKLEKRVQYMIEVLAQVRKDNFKDFP 258 (551)
Q Consensus 179 ~~te~~iEll~~lL~~~G~~LR~~dG~~L~~~~~~q~~~~l~~i~~~lr~~l~~~~~ssR~~fmie~l~dLr~n~~k~~~ 258 (551)
.||+++||+++.+|+.| |..|.+++ |.+++.||+|+|.|++++++++|++||||+++.+|+.+|+.+|
T Consensus 286 ~PTddSvevaI~flkec--------GakL~~VS----pr~~n~IfErlR~ILhe~Eld~rvqy~iEtlf~iRkdkfk~~p 353 (739)
T KOG2140|consen 286 RPTDDSVEVAIAFLKEC--------GAKLAEVS----PRALNGIFERLRYILHEGELDRRVQYMIETLFQIRKDKFKSHP 353 (739)
T ss_pred CCCCchHHHHHHHHHHH--------HHHHHHhC----hHHHhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHhhccCC
Confidence 99999999999999999 99999999 9999999999999999999999999999999999999999999
Q ss_pred CcccccCCCCcCCcceeEEecCCCCChhhhhccccCChhhhhhhhhhhhccccccCCCCCCCCCCCCCcccchhhhhh-h
Q psy7791 259 DVIEDLDLVPEEDKFTHLMTLDGVKDTQDILNVFQYDPEYLMNEEKYTTLRREILGDEDEDDEDGDDEEDEDEEESEA-E 337 (551)
Q Consensus 259 ~~~~~l~~v~~~~~~~~~~~l~~~~~~~~~L~~~~~d~~~~~~e~~~~~gkwwivG~~~~~~~~~~~~~~~~~~~~~~-~ 337 (551)
++.++||+|+++||+||.+.+++..+++..|++|++||+|.++|.+|+..|..|+|.+...++++++++++++++.+. +
T Consensus 354 ~v~~~LDlvee~dq~tH~l~l~de~dpe~~L~vFk~dp~f~ene~kydaikkeiLgn~dsen~d~~~~s~E~~~eee~e~ 433 (739)
T KOG2140|consen 354 AVLEELDLVEEEDQITHSLSLEDEDDPEKELGVFKKDPNFEENEEKYDAIKKEILGNEDSENEDDEDGSSEDDDEEEDES 433 (739)
T ss_pred ccccccCccchhhheeeeeecccccChhhhhcccccCccHHHHHHHHHHHHHHHhcCCcccccccccccccccccccccc
Confidence 999999999999999999999999999999999999999999999999999999999887555544444333322221 2
Q ss_pred hhhccchhhhhhhhccccchhhhhhhhhcccCCCHHHHHHHHHccCCCCCCccchheeeeeccccccccccccccchhhH
Q psy7791 338 EGEKENKETIIDNTETNLVALRRTIYLTIHSSLDFEECAHKLLRMQLKPGQESELCHIVHIDTSLWGLFGDQLRTYEKFF 417 (551)
Q Consensus 338 ~~~~~~~~~l~d~~~mn~td~RR~If~~ImSS~d~~dA~~kLlkL~lk~~qerEi~~vl~i~C~~~~~~c~qEktyNpyY 417 (551)
.++.++.++|.|+|..|++++||+||++||||.||+||+|||||+.++++|+.|+|.|| |+| |.||+||.+||
T Consensus 434 ~ee~~e~~qI~D~T~~Nlv~frr~IYLti~SSldfeEaaHKLLKmkip~~q~~elc~mi-i~c------c~QerTy~kFY 506 (739)
T KOG2140|consen 434 VEEDEEKLQIIDMTETNLVNFRRTIYLTIQSSLDFEEAAHKLLKMKIPESQEKELCNMI-IDC------CAQERTYEKFY 506 (739)
T ss_pred cccccccceeeccccchhHHhhhhheeeeeccCcHHHHHHHHHhccCCchhhHHHHHHH-HHH------hhhHHHHHHHH
Confidence 23445688999999999999999999999999999999999999999999999999999 999 99999999999
Q ss_pred HHHHHHHhhcchhhHHHHHHHHHHHhhhhhcccccccccchhhhhhhhhhcchhhhhhhhccccccchhhHHhhHHHHHH
Q psy7791 418 GLLAQRFCQINKMYVAPLEQIFRESYSTVHRLDINKLRDDVCVINVVVKINGLTRLQFLYLSSNVVSNYDKLRNVAKFFA 497 (551)
Q Consensus 418 ~~la~rlC~~~~~~~~tfq~~fwd~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~Nlak~~a 497 (551)
|+|++|||..++.||.+|..||.+.|.+||++++|+ |||+|||||
T Consensus 507 glL~eRfc~l~r~~q~~fe~~f~q~YstIhr~Etnk-----------------------------------LRnlakffa 551 (739)
T KOG2140|consen 507 GLLGERFCMLHREWQEAFEKCFKQQYSTIHRYETNK-----------------------------------LRNLAKFFA 551 (739)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHH-----------------------------------HHHHHHHHH
Confidence 999999999999999999999999999999999999 999999999
Q ss_pred HHHhhCccccccccceecCccccCcchHHHHHHHHHHHHHHhcHHHHhhhhcCC
Q psy7791 498 HQLFTDAIGWHVLSCIHLNEEETTSSGRIFIKILFQELSEYMGLSKLNQKIKDP 551 (551)
Q Consensus 498 ~Ll~~~~l~l~vLk~i~~~e~~t~~~~riF~k~Lf~el~~~lg~~~l~~~l~~~ 551 (551)
||+++++|||.||++|.+||++|++++|||||+|||||+++||+++|++||+||
T Consensus 552 hLlstd~lpw~vl~~ikLTEEdTtsssRIfiKilFqELve~lGl~~L~~RL~dp 605 (739)
T KOG2140|consen 552 HLLSTDALPWDVLACIKLTEEDTTSSSRIFIKILFQELVEALGLDKLNERLNDP 605 (739)
T ss_pred HHhcccccchHHHHHhhcccccCCccceehHHHHHHHHHHHhChHHHHHHhcCc
Confidence 999999999999999999999999999999999999999999999999999998
No 2
>KOG2141|consensus
Probab=100.00 E-value=1.4e-94 Score=776.46 Aligned_cols=455 Identities=22% Similarity=0.312 Sum_probs=361.6
Q ss_pred CCCCCCccc-ccCCCCCCcccChHHhhhhhhhcCCcchhHHHHhhHHHHHHHHhHHhhhcCCCcHHHHHHHHHHHHhhhh
Q psy7791 10 SSEPKTSTN-ILSSKTGGAYIPPAKLKLMQQSISDKSSVEYQRISWETLKKSIHGSVNKVNTGNIGIIARKLFQENIIRG 88 (551)
Q Consensus 10 ~~~~~~~~~-~~~~~~~~kYVPP~~~r~~~~~~~d~~see~Q~~~w~~L~r~I~glLNKLs~~Ni~~i~~eL~~~n~~~g 88 (551)
++++.+++. .....++.||||||+|.++. +++.+|+. .+|+|+|+|+|||||++||..|+.+|-.++..++
T Consensus 279 ~~~~~~e~~~~~~~~s~sKYvPPslRkkl~---~~~~sE~l-----~rl~rkv~g~LNKLSdaNi~~I~~~i~~Ly~~~s 350 (822)
T KOG2141|consen 279 ALKKSEEPEYLRKINSSSKYVPPSLRKKLE---TSSESEQL-----QRLRRKVNGSLNKLSDANIIKIIAGIAELYMNNS 350 (822)
T ss_pred ccccCCCcccccccccccccCCHHHHHHhc---CccchHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 334444433 33456788999999887774 45566665 4999999999999999999999987777776666
Q ss_pred hhHHHHH----HHHH----HhcCCchHHHHHHHHHHHHccC-CchHHHHHHHHHHHHHHHHhcc---C--ccchhhHHHH
Q psy7791 89 RGLLTRT----ILQA----QAASPTFTNVYAALVDIINSKF-PSIGELLLNRCIQQFKRSFKRN---D--KALCINSVTF 154 (551)
Q Consensus 89 r~ll~~~----Il~~----~~~~~~~~~vyAaLia~L~~~~-pevG~~ll~~lv~~F~~~~~~~---d--~k~~~n~~~f 154 (551)
|..++.+ |.++ +...+.++.+||||++.+|+.+ .+||+||++..|+.|.+.|+.. + .|.|.|++.|
T Consensus 351 r~~v~~sLtk~l~~~~~~~~~~ld~~~~~y~AL~~~l~~~vg~eigahf~q~~ve~f~~~~~~~~~~~~~~K~~~Nl~~~ 430 (822)
T KOG2141|consen 351 RYDVTSSLTKLLLKALLGPFRLLDSLLTTYAALAAMLHTMVGNEIGAHFLQTFVEDFLKSYKEEEEMDLKDKSLNNIVLF 430 (822)
T ss_pred hhhHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcccccchhhhHHHH
Confidence 6654433 3332 3334568999999999999876 9999999999999999999864 2 7889999999
Q ss_pred HHHHHhcccccHHHHHHHHHHHhcCCCCCcHHHHHHHHHHhhhhhhcccCccccchh-hhcchHHHHHHHHHHHhhhcCC
Q psy7791 155 IAHLVNQQVAHEIIVLEILTLLVETPTNDSDFSLEPYSKHKLHHLRSLMCMPLWWIS-SIQSFQALESFFSTDVYNSSKG 233 (551)
Q Consensus 155 ia~Lynf~Vv~~~li~dii~~Lle~~te~~iEll~~lL~~~G~~LR~~dG~~L~~~~-~~q~~~~l~~i~~~lr~~l~~~ 233 (551)
+|||||||+++|.+|||||+.|.+++|+.++|+++.|+.+||++||+|||.+|++++ .+|+..+ ..-- .
T Consensus 431 l~ylynF~ivs~~LiydiI~kl~~~l~e~~ve~ll~ii~~~G~~LRkDDp~alk~~i~eiq~~a~---------~a~~-s 500 (822)
T KOG2141|consen 431 LSYLYNFGIVSCSLIYDIIRKLAENLNETNVEALLTIIANCGFSLRKDDPLALKDIITEIQSKAA---------SAKI-S 500 (822)
T ss_pred HHHHHHhhcccHHHHHHHHHHHHhchhhhhHHHHHHHHHHccchhcCCChHHHHHHHHHHHHHhh---------cCCc-c
Confidence 999999999999999999999999999999999999999999999999999888876 3443211 1111 1
Q ss_pred CchhHHHHHHHHHHHHHHcCCcCCCCcccccCCCCcCCccee-EEecCCC---CChhhhhccccCChhhhhhhhhhhhcc
Q psy7791 234 KLEKRVQYMIEVLAQVRKDNFKDFPDVIEDLDLVPEEDKFTH-LMTLDGV---KDTQDILNVFQYDPEYLMNEEKYTTLR 309 (551)
Q Consensus 234 ~~ssR~~fmie~l~dLr~n~~k~~~~~~~~l~~v~~~~~~~~-~~~l~~~---~~~~~~L~~~~~d~~~~~~e~~~~~gk 309 (551)
-.+.|++||+|+|.+||||+.++.|...++. | ..+| ..+..+. .+....|.+.. .+...+| ++||
T Consensus 501 ~~~pR~rFmleti~aLKnN~~kki~~~d~e~--v----e~lrk~~k~l~~~~~s~~~~~l~vTl--edll~ae---~kGr 569 (822)
T KOG2141|consen 501 AISPRLRFMLETISALKNNKLKKIPYADPER--V----ENLRKLKKALGSSASSSVSLPLSVTL--EDLLHAE---QKGR 569 (822)
T ss_pred ccchHHHHHHHHHHHHhcCCCcCCCcCChHH--H----HHHHHHHHHHHhccchhhhccccccH--HHhhChH---hcCc
Confidence 2589999999999999999999987654321 2 1122 1122221 22223333432 2444455 6899
Q ss_pred ccccCCCCCCCCCCCCCcccchhh--h-hhhhhhccchhhhhhhhccccchhhhhhhhhcccCCCHHHHHHHHHccCCCC
Q psy7791 310 REILGDEDEDDEDGDDEEDEDEEE--S-EAEEGEKENKETIIDNTETNLVALRRTIYLTIHSSLDFEECAHKLLRMQLKP 386 (551)
Q Consensus 310 wwivG~~~~~~~~~~~~~~~~~~~--~-~~~~~~~~~~~~l~d~~~mn~td~RR~If~~ImSS~d~~dA~~kLlkL~lk~ 386 (551)
|||||++|.|++..........+. . +.+....++++++|++|||| |++||+|||+||||+||.|||+|||||+||+
T Consensus 570 WWlVGsaw~g~~~~~~s~~~~~d~~~~k~~~gs~~~kmL~lArkqrMN-TdiRr~IFcsImsaeDyiDAFEklLkL~LK~ 648 (822)
T KOG2141|consen 570 WWLVGSAWRGNEQFMGSINTASDSAKSKKAEGSFADKMLELARKQRMN-TDIRRAIFCSIMSAEDYIDAFEKLLKLSLKG 648 (822)
T ss_pred eEEecchhcCCcccccccchHhHHhhhhcccCCccHHHHHHHHHhhcc-hHhhhhheeeeecchHHHHHHHHHHhccCCC
Confidence 999999999976633211111111 1 11223456788999999999 9999999999999999999999999999999
Q ss_pred CCccchheeeeeccccccccccccccchhhHHHHHHHHhhcchhhHHHHHHHHHHHhhhhhcccccccccchhhhhhhhh
Q psy7791 387 GQESELCHIVHIDTSLWGLFGDQLRTYEKFFGLLAQRFCQINKMYVAPLEQIFRESYSTVHRLDINKLRDDVCVINVVVK 466 (551)
Q Consensus 387 ~qerEi~~vl~i~C~~~~~~c~qEktyNpyY~~la~rlC~~~~~~~~tfq~~fwd~~~~i~~~~~~~~~~~~~~~~~~~~ 466 (551)
+|+|||+||| ||| |+|||+||||||+||.|||.+++.|++||||++||+|++++.+..
T Consensus 649 ~Q~rEI~~Vl-lhC------~l~EK~yNpfYa~lA~KfCe~~~~~~~tfQF~~WD~f~ele~ls~--------------- 706 (822)
T KOG2141|consen 649 KQEREIARVL-LHC------CLNEKTYNPFYALLALKFCEFNKNLKKTFQFALWDRFKELEQLSL--------------- 706 (822)
T ss_pred cchHHHHHHH-HHH------HhhhcccchHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhhhcch---------------
Confidence 9999999999 999 999999999999999999999999999999999999999998765
Q ss_pred hcchhhhhhhhccccccchhhHHhhHHHHHHHHHhhCccccccccceecCccccCcchHHHHHHHHHHHHHH
Q psy7791 467 INGLTRLQFLYLSSNVVSNYDKLRNVAKFFAHQLFTDAIGWHVLSCIHLNEEETTSSGRIFIKILFQELSEY 538 (551)
Q Consensus 467 ~~~~~~~~~~~~~~~~~~~~~~l~Nlak~~a~Ll~~~~l~l~vLk~i~~~e~~t~~~~riF~k~Lf~el~~~ 538 (551)
.|++|||+|+||||++.++||+|||+|+|++++ +....|++.+|..|+-.
T Consensus 707 --------------------~ri~nLa~l~a~Li~~~~lsLtVLK~Vdfm~l~--~~~~~fl~~~l~~l~l~ 756 (822)
T KOG2141|consen 707 --------------------FRISNLAKLLASLISNAVLSLTVLKHVDFMELN--ARRTTFLKKLLFGLILE 756 (822)
T ss_pred --------------------hhHhHHHHHHHHHHHhcccceeeeeeccHhhcC--hHHHHHHHHHHHHHHhc
Confidence 449999999999999999999999999999876 55778888777777654
No 3
>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=99.93 E-value=1.6e-25 Score=215.05 Aligned_cols=183 Identities=27% Similarity=0.405 Sum_probs=165.3
Q ss_pred HHHhHHhhhcCCCcHHHHHHHHHHHHhhh---hhhHHHHHHHHHHhcCCchHHHHHHHHHHHHccCC-chHHHHHHHHHH
Q psy7791 59 KSIHGSVNKVNTGNIGIIARKLFQENIIR---GRGLLTRTILQAQAASPTFTNVYAALVDIINSKFP-SIGELLLNRCIQ 134 (551)
Q Consensus 59 r~I~glLNKLs~~Ni~~i~~eL~~~n~~~---gr~ll~~~Il~~~~~~~~~~~vyAaLia~L~~~~p-evG~~ll~~lv~ 134 (551)
|+|+|++||||++|++.++.++...+... ....+++.|++.+...|.++++||+||+.|+...| +|+..++++|+.
T Consensus 2 r~v~~~lnklt~~n~~~~~~~l~~~~~~~~~~~~~~i~~~i~~~a~~~~~~~~~~a~l~~~l~~~~~~~f~~~ll~~~~~ 81 (209)
T PF02854_consen 2 RKVRGILNKLTPSNFESIIDELIKLNWSDDPETLKEIVKLIFEKAVEEPNFSPLYARLCAALNSRFPSEFRSLLLNRCQE 81 (209)
T ss_dssp HHHHHHHHHCSSTTHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHSGGGHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred chHHHHHHHCCHHHHHHHHHHHHHHHhhccHHHHHHHHHHHhhhhhcCchHHHHHHHHHHHHhccchhhHHHHHHHHHHH
Confidence 78999999999999999999999888765 45678899999988899999999999999999998 999999999999
Q ss_pred HHHH--------HHhccCccchhhHHHHHHHHHhcccccHHHHHHHHHHHhcCCCC--------CcHHHHHHHHHHhhhh
Q psy7791 135 QFKR--------SFKRNDKALCINSVTFIAHLVNQQVAHEIIVLEILTLLVETPTN--------DSDFSLEPYSKHKLHH 198 (551)
Q Consensus 135 ~F~~--------~~~~~d~k~~~n~~~fia~Lynf~Vv~~~li~dii~~Lle~~te--------~~iEll~~lL~~~G~~ 198 (551)
.|.. ......+.+..|.++|||+||+++|+++.++++++..|+...++ .+||++|.+|++|
T Consensus 82 ~f~~~~~~~~~~~~~~~~~~~~~~~~~fl~eL~~~~vv~~~~i~~~l~~ll~~~~~~~~~~~~~~~ie~~~~lL~~~--- 158 (209)
T PF02854_consen 82 EFEERYSNEELEENRQSSKQRRRGNIRFLAELFNFGVVSEKIIFDILRELLSDGTDECQPPPDEENIECLCTLLKTC--- 158 (209)
T ss_dssp HHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHHTSHHCCHHTCHHHHHHHHHHHHHH---
T ss_pred HHHHhhhhhhHHHHHHHHHHHHhhhhhHHHhhHhhccccchhHHHHHHHHHhcccccccCCCcHhHHHHHHHHHHHH---
Confidence 9999 33334577899999999999999999999999999999987766 8999999999999
Q ss_pred hhcccCcccc--chhhhcchHHHHHHHHHHHhhhcC---CCchhHHHHHHHHHHHHHHcC
Q psy7791 199 LRSLMCMPLW--WISSIQSFQALESFFSTDVYNSSK---GKLEKRVQYMIEVLAQVRKDN 253 (551)
Q Consensus 199 LR~~dG~~L~--~~~~~q~~~~l~~i~~~lr~~l~~---~~~ssR~~fmie~l~dLr~n~ 253 (551)
|..|. ... +..++.+|+.++..... +.++.|++||+++++++|+||
T Consensus 159 -----G~~l~~~~~~----~~~l~~~~~~~~~~~~~~~~~~~~~r~~~~l~~l~~lr~~~ 209 (209)
T PF02854_consen 159 -----GKKLENSEES----PKALDEIFERLQKYANSKKDPNLSSRIRFMLEDLIELRNNK 209 (209)
T ss_dssp -----HHHHHHCHHH----HHHHHHHHHHHHHHHHHCHSSSSSHHHHHHHHHHHHHHHTC
T ss_pred -----HHHHhcCCCc----hhHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHHHHhcCC
Confidence 55555 445 88899999999999876 899999999999999999986
No 4
>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=99.93 E-value=4e-25 Score=212.31 Aligned_cols=183 Identities=28% Similarity=0.373 Sum_probs=165.7
Q ss_pred HHHhHHhhhcCCCcHHHHHHHHHHHHhhhh--hhHHHHHHHHHHhcCCchHHHHHHHHHHHHccCCchHHHHHHHHHHHH
Q psy7791 59 KSIHGSVNKVNTGNIGIIARKLFQENIIRG--RGLLTRTILQAQAASPTFTNVYAALVDIINSKFPSIGELLLNRCIQQF 136 (551)
Q Consensus 59 r~I~glLNKLs~~Ni~~i~~eL~~~n~~~g--r~ll~~~Il~~~~~~~~~~~vyAaLia~L~~~~pevG~~ll~~lv~~F 136 (551)
++++|++||||++|++.++.+|...+...+ ++.+++.+++.+...|.++++||.||+.+|...|+||+.++++++..|
T Consensus 2 ~~v~~~lnkLs~~n~~~~~~~l~~~~~~~~~~~~~l~~~i~~~~~~~~~~~~~ya~L~~~l~~~~~~f~~~ll~~~~~~f 81 (200)
T smart00543 2 KKVKGLINKLSPSNFESIIKELLKLNNSDKNLRKYILELIFEKAVEEPNFIPAYARLCALLNAKNPDFGSLLLERLQEEF 81 (200)
T ss_pred hHHHHHHhhCCHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 689999999999999999999998887643 567888999998889999999999999999999999999999999999
Q ss_pred HH---HHhccCccchhhHHHHHHHHHhcccccHHHHHHHHHHHhcCCCC-------CcHHHHHHHHHHhhhhhhcccCcc
Q psy7791 137 KR---SFKRNDKALCINSVTFIAHLVNQQVAHEIIVLEILTLLVETPTN-------DSDFSLEPYSKHKLHHLRSLMCMP 206 (551)
Q Consensus 137 ~~---~~~~~d~k~~~n~~~fia~Lynf~Vv~~~li~dii~~Lle~~te-------~~iEll~~lL~~~G~~LR~~dG~~ 206 (551)
+. .....+++++.|.++|||+||+++|+++.++++++..|+..+++ .++|+++.+|++| |..
T Consensus 82 ~~~~e~~~~~~~~~~~~~i~fl~eL~~~~~i~~~~i~~~l~~ll~~~~~~~~~~~~~~ve~l~~lL~~~--------G~~ 153 (200)
T smart00543 82 EKGLESEEESDKQRRLGLVRFLGELYNFQVLTSKIILELLKELLNDLTKLDPPRSDFSVECLLSLLPTC--------GKD 153 (200)
T ss_pred HHHHHHHHHHhhhhHHhHHHHHHHHHHcccCcHHHHHHHHHHHHhccCCCCCCCcHHHHHHHHHHHHHh--------hHH
Confidence 98 44555678899999999999999999999999999999998876 7999999999999 666
Q ss_pred cc-chhhhcchHHHHHHHHHHHhhhcCC---CchhHHHHHHHHHHHHHHcC
Q psy7791 207 LW-WISSIQSFQALESFFSTDVYNSSKG---KLEKRVQYMIEVLAQVRKDN 253 (551)
Q Consensus 207 L~-~~~~~q~~~~l~~i~~~lr~~l~~~---~~ssR~~fmie~l~dLr~n~ 253 (551)
|. ... |..++.+++.++...... ..+.|++||++++.++|+|+
T Consensus 154 l~~~~~----~~~~~~~l~~l~~~~~~~~~~~~~~r~~~~l~~l~~l~~~~ 200 (200)
T smart00543 154 LEREKS----PKLLDEILERLQDYLLKKDKTELSSRLRFMLELLIELRKNK 200 (200)
T ss_pred HcCccc----HHHHHHHHHHHHHHHhcccccCCChHHHHHHHHHHHHhhCc
Confidence 66 566 888999999999998765 78999999999999999974
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=99.75 E-value=1.1e-18 Score=154.68 Aligned_cols=109 Identities=26% Similarity=0.481 Sum_probs=101.6
Q ss_pred hhhhhhhhcccCC---CHHHHHHHHHccCCCCCCccchheeeeeccccccccccccc-cchhhHHHHHHHHhhcchhhHH
Q psy7791 358 LRRTIYLTIHSSL---DFEECAHKLLRMQLKPGQESELCHIVHIDTSLWGLFGDQLR-TYEKFFGLLAQRFCQINKMYVA 433 (551)
Q Consensus 358 ~RR~If~~ImSS~---d~~dA~~kLlkL~lk~~qerEi~~vl~i~C~~~~~~c~qEk-tyNpyY~~la~rlC~~~~~~~~ 433 (551)
+||+||.+||++. |+.||+++|.+|+++ .+.+|+|+++ |+| |++++ +|+|||+.|+++||+.+..++.
T Consensus 1 ~~k~i~~~l~ey~~~~D~~ea~~~l~~L~~~-~~~~~vv~~~-i~~------~le~~~~~~~~~~~Ll~~L~~~~~~~~~ 72 (113)
T smart00544 1 LKKKIFLIIEEYLSSGDTDEAVHCLLELKLP-EQHHEVVKVL-LTC------ALEEKRTYREMYSVLLSRLCQANVISTK 72 (113)
T ss_pred ChhHHHHHHHHHHHcCCHHHHHHHHHHhCCC-cchHHHHHHH-HHH------HHcCCccHHHHHHHHHHHHHHcCCcCHH
Confidence 5899999998877 999999999999999 7999999999 999 99995 8999999999999999999999
Q ss_pred HHHHHHHHHhhhhhcccccccccchhhhhhhhhhcchhhhhhhhccccccchhhHHhhHHHHHHHHHhhCccc
Q psy7791 434 PLEQIFRESYSTVHRLDINKLRDDVCVINVVVKINGLTRLQFLYLSSNVVSNYDKLRNVAKFFAHQLFTDAIG 506 (551)
Q Consensus 434 tfq~~fwd~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~Nlak~~a~Ll~~~~l~ 506 (551)
+|+++||+.++.+++++..- ++...|+|+|+|++++.|+||
T Consensus 73 ~~~~~f~~~~~~l~dl~~D~--------------------------------P~a~~~la~~~a~~v~~~~l~ 113 (113)
T smart00544 73 QFEKGFWRLLEDIEDLELDI--------------------------------PNAWRNLAEFVARLISDGILP 113 (113)
T ss_pred HHHHHHHHHHhhChhhhccc--------------------------------ccHHHHHHHHHHHHHHcCCCC
Confidence 99999999999999887632 556999999999999999986
No 6
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=99.65 E-value=5.7e-17 Score=143.47 Aligned_cols=109 Identities=17% Similarity=0.384 Sum_probs=99.6
Q ss_pred hhhhhhhhcccCC---CHHHHHHHHHccCCCCCCccchheeeeecccccccccccc-ccchhhHHHHHHHHhhcchhhHH
Q psy7791 358 LRRTIYLTIHSSL---DFEECAHKLLRMQLKPGQESELCHIVHIDTSLWGLFGDQL-RTYEKFFGLLAQRFCQINKMYVA 433 (551)
Q Consensus 358 ~RR~If~~ImSS~---d~~dA~~kLlkL~lk~~qerEi~~vl~i~C~~~~~~c~qE-ktyNpyY~~la~rlC~~~~~~~~ 433 (551)
+||+||.+||++. |++||+++|.+|+++ .+.+++++++ |+| |+++ ++|++||+.|+.+||..+...+.
T Consensus 1 ~rk~i~~~l~ey~~~~d~~ea~~~l~el~~~-~~~~~vv~~~-l~~------~le~~~~~r~~~~~Ll~~L~~~~~~~~~ 72 (113)
T PF02847_consen 1 LRKKIFSILMEYFSSGDVDEAVECLKELKLP-SQHHEVVKVI-LEC------ALEEKKSYREYYSKLLSHLCKRKLISKE 72 (113)
T ss_dssp HHHHHHHHHHHHHHHT-HHHHHHHHHHTT-G-GGHHHHHHHH-HHH------HHTSSHHHHHHHHHHHHHHHHTTSS-HH
T ss_pred ChHHHHHHHHHHhcCCCHHHHHHHHHHhCCC-ccHHHHHHHH-HHH------HhhccHHHHHHHHHHHHHHHhcCCCCHH
Confidence 6999999999999 999999999999999 9999999999 999 9999 99999999999999999999999
Q ss_pred HHHHHHHHHhhhhhcccccccccchhhhhhhhhhcchhhhhhhhccccccchhhHHhhHHHHHHHHHhhCccc
Q psy7791 434 PLEQIFRESYSTVHRLDINKLRDDVCVINVVVKINGLTRLQFLYLSSNVVSNYDKLRNVAKFFAHQLFTDAIG 506 (551)
Q Consensus 434 tfq~~fwd~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~Nlak~~a~Ll~~~~l~ 506 (551)
+|+++||+.++.++++..+- ++...|+|+|+|+++..|+||
T Consensus 73 ~~~~gf~~~l~~l~Dl~~D~--------------------------------P~~~~~la~~~~~~i~~~~lp 113 (113)
T PF02847_consen 73 QFQEGFEDLLESLEDLELDI--------------------------------PKAPEYLAKFLARLIADGILP 113 (113)
T ss_dssp HHHHHHHHHHHHHHHHHHHS--------------------------------TTHHHHHHHHHHHHHHTTSS-
T ss_pred HHHHHHHHHHhHhhhccccc--------------------------------hHHHHHHHHHHHHHHHcCCcC
Confidence 99999999999999877542 566999999999999999997
No 7
>KOG0401|consensus
Probab=99.40 E-value=5.8e-13 Score=156.18 Aligned_cols=220 Identities=20% Similarity=0.284 Sum_probs=171.5
Q ss_pred CCCCcccChHHhhhhhhhcCCcchhHHHHhhHHHHHHHHhHHhhhcCCCcHHHHHHHHHHHHhhhhh--hHHHHHHHHHH
Q psy7791 23 KTGGAYIPPAKLKLMQQSISDKSSVEYQRISWETLKKSIHGSVNKVNTGNIGIIARKLFQENIIRGR--GLLTRTILQAQ 100 (551)
Q Consensus 23 ~~~~kYVPP~~~r~~~~~~~d~~see~Q~~~w~~L~r~I~glLNKLs~~Ni~~i~~eL~~~n~~~gr--~ll~~~Il~~~ 100 (551)
...+.+.|..++.+. . .+.+.+..+...-+.+.++|++++|++++.++.....++...+..... +-+...|+...
T Consensus 318 ~~~~~~~ps~k~a~~-~--~~~~~~~~~~~~~~el~~~vrsilnkltp~~~~~l~~q~~~~~i~t~~~l~~vi~~vfdkA 394 (970)
T KOG0401|consen 318 FAQKAPSPSPKRAKS-K--SDQGAERKDVELKEELAKRVRSLLNKLTPERKELLIEQLIELNVDTDDALKEVIELVFDKA 394 (970)
T ss_pred hccCCCCCcchhhcc-c--cccccccchhHHHHHHHHHHhhhcCCCchHHHHHHHHHHHhhccCcHHHHhHHHHHHHHhh
Confidence 344555565544321 1 122223333344579999999999999999999999988876665432 34567788888
Q ss_pred hcCCchHHHHHHHHHHHHc-----cC------CchHHHHHHHHHHHHHHHH--hc---------cC------------cc
Q psy7791 101 AASPTFTNVYAALVDIINS-----KF------PSIGELLLNRCIQQFKRSF--KR---------ND------------KA 146 (551)
Q Consensus 101 ~~~~~~~~vyAaLia~L~~-----~~------pevG~~ll~~lv~~F~~~~--~~---------~d------------~k 146 (551)
..+|.|...||.||-.++. .. +.|-.+++.+|...|...- .. .+ ++
T Consensus 395 i~EP~f~~~yA~lc~~l~~~~~~~~~~~~~~~~~fr~~lL~rcq~~fe~~~~~~~~~~~~~~~~~~~e~~le~~k~~~~~ 474 (970)
T KOG0401|consen 395 INEPTFCAMYARLCFDLEGPPSEPELDMGGDEINFRRLLLNRCQKEFEGEDDKIADEYSEAEEPDELEEELEEEKYILRR 474 (970)
T ss_pred hcccccchhcchhcccccCCccCCCcCCCCCcccHHHHHHHHhHHHhhcccHHHHHHhhhhcCchhHHHHHHhccceecC
Confidence 8999999999999998876 11 4567899999999997654 11 01 46
Q ss_pred chhhHHHHHHHHHhcccccHHHHHHHHHHHhcC--CCCCcHHHHHHHHHHhhhhhhcccCccccchhhhcchHHHHHHHH
Q psy7791 147 LCINSVTFIAHLVNQQVAHEIIVLEILTLLVET--PTNDSDFSLEPYSKHKLHHLRSLMCMPLWWISSIQSFQALESFFS 224 (551)
Q Consensus 147 ~~~n~~~fia~Lynf~Vv~~~li~dii~~Lle~--~te~~iEll~~lL~~~G~~LR~~dG~~L~~~~~~q~~~~l~~i~~ 224 (551)
+..+.+.||++||..+++++.+++.|+..|+.. ++|.++|++|.++.++ |..+.... -++..+..+|.
T Consensus 475 rtlgn~~~ig~l~~~~ml~e~i~~~~v~~Ll~~~~~~ee~ie~lc~f~~ti--------g~~lD~~~--~s~r~md~~~~ 544 (970)
T KOG0401|consen 475 RTLGNFRFIGELFKLKMLTEKIVHACVQKLLSDDQPSEESIECLCRFLTTI--------GKKLDFSK--ESPRNMDEYFN 544 (970)
T ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhhhhHHhhhhcc--------cccccccC--cccchhHHHHH
Confidence 788889999999999999999999999999988 8899999999999999 88777542 11444677888
Q ss_pred HHHhhhcCCCchhHHHHHHHHHHHHHHcCCc
Q psy7791 225 TDVYNSSKGKLEKRVQYMIEVLAQVRKDNFK 255 (551)
Q Consensus 225 ~lr~~l~~~~~ssR~~fmie~l~dLr~n~~k 255 (551)
+++......+.+.|+|||+..+.++|.|+|.
T Consensus 545 ~~k~~~~~~~~s~r~RfM~~~~idlR~~~w~ 575 (970)
T KOG0401|consen 545 SMKNLKRKPQRSNRIRFMLQSVIDLRKSGWG 575 (970)
T ss_pred HHHHhhhhhhhccchhhhhcccccccccccc
Confidence 8888887889999999999999999999994
No 8
>KOG2051|consensus
Probab=99.20 E-value=1.4e-10 Score=132.09 Aligned_cols=180 Identities=15% Similarity=0.135 Sum_probs=140.0
Q ss_pred hHHhhhcCCCcHHHHHHHHHH-HHhhhhhhHHHHHHHHHHhcCCchHHHHHHHHHHHHccCCchHHHHHHHHHHHHHHHH
Q psy7791 62 HGSVNKVNTGNIGIIARKLFQ-ENIIRGRGLLTRTILQAQAASPTFTNVYAALVDIINSKFPSIGELLLNRCIQQFKRSF 140 (551)
Q Consensus 62 ~glLNKLs~~Ni~~i~~eL~~-~n~~~gr~ll~~~Il~~~~~~~~~~~vyAaLia~L~~~~pevG~~ll~~lv~~F~~~~ 140 (551)
.++=|.++.+=|+..+.+.+. +|....|.-++++++..+..+-.+.|.|+.|||.|+..+|+|..-|+..+-..|+...
T Consensus 432 ~~L~~~vsrdliD~~a~ef~~nlNtKa~RkrLvKal~~vprt~ldllPyYsRlVAtl~~~M~dvat~lv~~L~~eFr~~~ 511 (1128)
T KOG2051|consen 432 LDLPNCVSRDLIDQAAIEFCSNLNTKANRKRLVKALFVVPRTRLDLLPYYSRLVATLSKCMPDVATELVTMLRKEFRSHL 511 (1128)
T ss_pred ccCcchHHHHHHHHHHHHHHHHhccHHHHHHHHHhhhcccchhhhhhhHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence 334444445666667777665 7777778888888876655555689999999999999999999999999999999998
Q ss_pred hccCccchhh---HHHHHHHHHhcccccHHHHHHHHHHHhcCCCCCcHHHHHHHHHHhhhhhhcccCccccchhhhcchH
Q psy7791 141 KRNDKALCIN---SVTFIAHLVNQQVAHEIIVLEILTLLVETPTNDSDFSLEPYSKHKLHHLRSLMCMPLWWISSIQSFQ 217 (551)
Q Consensus 141 ~~~d~k~~~n---~~~fia~Lynf~Vv~~~li~dii~~Lle~~te~~iEll~~lL~~~G~~LR~~dG~~L~~~~~~q~~~ 217 (551)
.+++...... .++|||+|.+||+++...+|.|++.|+..|+.++||++|.+|.+| |..|-... -++-
T Consensus 512 hkK~q~~ietk~~~VrfIsEL~KF~lv~~~~if~cLk~ll~dF~~hnIEm~c~lLE~~--------GrfLlr~p--Et~l 581 (1128)
T KOG2051|consen 512 HKKAQINIETKLKIVRFISELCKFQLVPKFEIFSCLKMLLNDFTHHNIEMACVLLESC--------GRFLLRSP--ETKL 581 (1128)
T ss_pred hhhhhhhhhhhhhhhhhHHhhhhhCccChHHHHHHHHHHHHhcccccHHHHHHHHHhc--------chhhhcCh--hHHH
Confidence 8775433222 399999999999999999999999999999999999999999999 77776532 1123
Q ss_pred HHHHHHHHHHhhhcCCCchhHHHHHHHHHHHHHH
Q psy7791 218 ALESFFSTDVYNSSKGKLEKRVQYMIEVLAQVRK 251 (551)
Q Consensus 218 ~l~~i~~~lr~~l~~~~~ssR~~fmie~l~dLr~ 251 (551)
-++..++++++.-....+.+|-.-+||..+-+-+
T Consensus 582 rM~~~Le~i~rkK~a~~lDsr~~~~iENay~~~~ 615 (1128)
T KOG2051|consen 582 RMRVFLEQIKRKKRASALDSRQATLIENAYYLCN 615 (1128)
T ss_pred HHHHHHHHHHHHHHHhhhchHHHHHHHHhHHhcc
Confidence 4445666666554556678888888887776644
No 9
>KOG1104|consensus
Probab=98.16 E-value=6.3e-05 Score=84.45 Aligned_cols=192 Identities=15% Similarity=0.185 Sum_probs=136.0
Q ss_pred hhHHHHHHHHhHHhhhcCCC-------cHHHHHHHHHHHHhhhhhhHHHHHHHHHHhcCCchHHHHHHHHHHHHccCCch
Q psy7791 52 ISWETLKKSIHGSVNKVNTG-------NIGIIARKLFQENIIRGRGLLTRTILQAQAASPTFTNVYAALVDIINSKFPSI 124 (551)
Q Consensus 52 ~~w~~L~r~I~glLNKLs~~-------Ni~~i~~eL~~~n~~~gr~ll~~~Il~~~~~~~~~~~vyAaLia~L~~~~pev 124 (551)
..|+.+.+.+.+.+-++.+. |++..+.=|-+.... -+.-+.+.|.......|.-+++||.||..+|.+-++|
T Consensus 22 ~~~e~l~krl~~~i~~vg~~s~ss~e~~l~~l~~~l~~~~~~-~~~~iL~~L~~ca~~lP~K~~~yaTLvgllN~kn~~f 100 (759)
T KOG1104|consen 22 SPAETLEKRLESLIREVGEPSGSSVEDNLENLVAVLEADLEN-FKSKILDILNTCAVYLPEKITAYATLVGLLNLKNFNF 100 (759)
T ss_pred CcHHHHHHHHHHHHHhhcCCCCCcHHHhHHHHHHHHHhhHHH-HHHHHHHHHHHHHHHcccchhHHHHHHHHHhccchhh
Confidence 45789999999999999943 444444322222211 2233334444444457999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhccCccchhhHHHHHHHHHhcccccHHHHHHHHHHHhcCCCCCc---------HHHHHHHHHHh
Q psy7791 125 GELLLNRCIQQFKRSFKRNDKALCINSVTFIAHLVNQQVAHEIIVLEILTLLVETPTNDS---------DFSLEPYSKHK 195 (551)
Q Consensus 125 G~~ll~~lv~~F~~~~~~~d~k~~~n~~~fia~Lynf~Vv~~~li~dii~~Lle~~te~~---------iEll~~lL~~~ 195 (551)
|+.+++..+.+|......++..++.++++|++-|+|.+|+...-+..++..|++.-.+.+ +-+++.-|-..
T Consensus 101 g~~~v~~~~~~~q~sl~~~~~n~ar~llrfL~dL~~~~vl~~~sli~l~esl~~~~~e~~~Pqvr~D~~v~~vLs~lPw~ 180 (759)
T KOG1104|consen 101 GGEFVEYMIEELQESLKSGNWNEARYLLRFLSDLSNCHVLQADSLINLFESLLDAAIEENVPQVRRDYYVYCVLSSLPWF 180 (759)
T ss_pred HHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHhcCCccChHHHHHHHHHHHHHHHhhcCcchhhhHHHHHHHhccchh
Confidence 999999999999999999999999999999999999999999999999999987433322 22333333344
Q ss_pred hhhhhcccCccccchhhhcchHHHHHHHHHHHhhhcC-------------CC----chhHHHHHHHHHHHHHHcCCcC
Q psy7791 196 LHHLRSLMCMPLWWISSIQSFQALESFFSTDVYNSSK-------------GK----LEKRVQYMIEVLAQVRKDNFKD 256 (551)
Q Consensus 196 G~~LR~~dG~~L~~~~~~q~~~~l~~i~~~lr~~l~~-------------~~----~ssR~~fmie~l~dLr~n~~k~ 256 (551)
|..|.+ ++|..++.++..++.-+.- +. ...=+.-+...|-.+|+|+|.-
T Consensus 181 --------g~el~e----~~~~~~e~ll~~ie~Yl~~R~~shi~lL~vw~~~~~~~qeeyle~L~~qI~~lr~n~w~e 246 (759)
T KOG1104|consen 181 --------GRELNE----KKPTEMEELLVYIEIYLKKRKKSHINLLNVWSGEPDHPQEEYLELLWAQIQKLRQNDWAE 246 (759)
T ss_pred --------hhhhcc----cchHHHHHHHHHHHHHHHHhcccccchhhcCCCCCCchHHHHHHHHHHHHHHHHhcCccc
Confidence 455544 3477888877776655421 11 1122345666677899999963
No 10
>KOG2051|consensus
Probab=97.93 E-value=0.00027 Score=81.95 Aligned_cols=140 Identities=11% Similarity=0.096 Sum_probs=103.6
Q ss_pred HHHHHhHHhh-hcCCCcHHHHHHHHHHHHhhh--hhhHHHHHHHHHHhcCCchHHHHHHHHHHHHccCCchHHHHHHHHH
Q psy7791 57 LKKSIHGSVN-KVNTGNIGIIARKLFQENIIR--GRGLLTRTILQAQAASPTFTNVYAALVDIINSKFPSIGELLLNRCI 133 (551)
Q Consensus 57 L~r~I~glLN-KLs~~Ni~~i~~eL~~~n~~~--gr~ll~~~Il~~~~~~~~~~~vyAaLia~L~~~~pevG~~ll~~lv 133 (551)
++.-|+-++- .|+..|+..++.-+-.+.-.. -...+.+.++..=...-+-++..|.|+|+|....|+||-+.|..+.
T Consensus 630 ~~efiR~Li~~dL~k~tvd~~lkllRkl~W~D~e~~~yli~~~~k~w~iky~~i~~lA~llaGL~~y~~~fvi~VID~vl 709 (1128)
T KOG2051|consen 630 MQEFIRYLIRSDLSKDTVDRVLKLLRKLDWSDPEVKQYLISCFSKPWKIKYQNIHALASLLAGLSSYHPEFVIHVIDHVL 709 (1128)
T ss_pred HHHHHHHHHHHHhccccHHHHHHHHHhcccccHHHHHHHHHHhhhhhccccccHHHHHHHHHHHHhhchhhhhhhHHHHH
Confidence 3445555555 677788887776554433211 1344555555543334456778899999999999999999999999
Q ss_pred HHHHHHHhccC---ccchhhHHHHHHHHHhcccccHHHHHHHHHHHhc--CCCC------------CcHHHHHHHHHHhh
Q psy7791 134 QQFKRSFKRND---KALCINSVTFIAHLVNQQVAHEIIVLEILTLLVE--TPTN------------DSDFSLEPYSKHKL 196 (551)
Q Consensus 134 ~~F~~~~~~~d---~k~~~n~~~fia~Lynf~Vv~~~li~dii~~Lle--~~te------------~~iEll~~lL~~~G 196 (551)
+..+.+..-|+ +-.+..+++|||+||||.++.+.+|+..|-.++- .++. .-|-++|.+|.+||
T Consensus 710 E~Ir~glEin~~~~nQrriA~aryL~ELynfemvds~vIl~tLy~~i~~g~~~~~~~~~ldppddlFRirlV~~lL~tc~ 789 (1128)
T KOG2051|consen 710 EDIRPGLEINDYVSNQRRIALARYLGELYNFEMVDSDVILNTLYHLISLGHFENLTPSALDPPDDLFRIRLVCMLLQTCG 789 (1128)
T ss_pred HHHHhhhhcCcHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHhcccccCCCCcccCCChHHHHHHHHHHHHHHHcc
Confidence 99998888766 4568899999999999999999999999988873 2222 25889999999994
No 11
>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=95.24 E-value=0.016 Score=55.32 Aligned_cols=106 Identities=12% Similarity=0.201 Sum_probs=80.9
Q ss_pred ccCCCHHHHHHHHHccCCCC--CCccchheeeeeccccccccccccccchhhHHHHHHHHhhcch-hhHHHHHHHHHHHh
Q psy7791 367 HSSLDFEECAHKLLRMQLKP--GQESELCHIVHIDTSLWGLFGDQLRTYEKFFGLLAQRFCQINK-MYVAPLEQIFRESY 443 (551)
Q Consensus 367 mSS~d~~dA~~kLlkL~lk~--~qerEi~~vl~i~C~~~~~~c~qEktyNpyY~~la~rlC~~~~-~~~~tfq~~fwd~~ 443 (551)
.|..+++....-|.++.... .....+++.+ ++| |.++..|-|+|+-++..++.... .|...+-..+.+.|
T Consensus 11 lt~~n~~~~~~~l~~~~~~~~~~~~~~i~~~i-~~~------a~~~~~~~~~~a~l~~~l~~~~~~~f~~~ll~~~~~~f 83 (209)
T PF02854_consen 11 LTPSNFESIIDELIKLNWSDDPETLKEIVKLI-FEK------AVEEPNFSPLYARLCAALNSRFPSEFRSLLLNRCQEEF 83 (209)
T ss_dssp CSSTTHHHHHHHHHHHHHHSCHHHHHHHHHHH-HHH------HHHSGGGHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHhhccHHHHHHHHHHH-hhh------hhcCchHHHHHHHHHHHHhccchhhHHHHHHHHHHHHH
Confidence 34677777888887776554 5567799999 999 99999999999999999999888 88888877777777
Q ss_pred hhhh---cccccccccchhhhhhhhhhcchhhhhhhhccccccchhhHHhhHHHHHHHHHhhCccccc
Q psy7791 444 STVH---RLDINKLRDDVCVINVVVKINGLTRLQFLYLSSNVVSNYDKLRNVAKFFAHQLFTDAIGWH 508 (551)
Q Consensus 444 ~~i~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~Nlak~~a~Ll~~~~l~l~ 508 (551)
..-. ..+.+ ....-+|..+..+|+|.|+..+.++-.
T Consensus 84 ~~~~~~~~~~~~-----------------------------~~~~~~~~~~~~~fl~eL~~~~vv~~~ 122 (209)
T PF02854_consen 84 EERYSNEELEEN-----------------------------RQSSKQRRRGNIRFLAELFNFGVVSEK 122 (209)
T ss_dssp HHHT-HHHHHHH-----------------------------HHHHHHHHHHHHHHHHHHHHTTSSCHH
T ss_pred HHhhhhhhHHHH-----------------------------HHHHHHHHhhhhhHHHhhHhhccccch
Confidence 6521 11100 011256799999999999999988764
No 12
>smart00543 MIF4G Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)
Probab=93.65 E-value=0.057 Score=51.51 Aligned_cols=107 Identities=9% Similarity=0.171 Sum_probs=79.6
Q ss_pred CCCHHHHHHHHHccCCCC-CCccchheeeeeccccccccccccccchhhHHHHHHHHhhcchhhHHHHHHHHHHHhhhh-
Q psy7791 369 SLDFEECAHKLLRMQLKP-GQESELCHIVHIDTSLWGLFGDQLRTYEKFFGLLAQRFCQINKMYVAPLEQIFRESYSTV- 446 (551)
Q Consensus 369 S~d~~dA~~kLlkL~lk~-~qerEi~~vl~i~C~~~~~~c~qEktyNpyY~~la~rlC~~~~~~~~tfq~~fwd~~~~i- 446 (551)
..+++....-|.++.... ....++++.+ ++| ...+..|-|+|+.++..+......|...+-..+.+.|...
T Consensus 13 ~~n~~~~~~~l~~~~~~~~~~~~~l~~~i-~~~------~~~~~~~~~~ya~L~~~l~~~~~~f~~~ll~~~~~~f~~~~ 85 (200)
T smart00543 13 PSNFESIIKELLKLNNSDKNLRKYILELI-FEK------AVEEPNFIPAYARLCALLNAKNPDFGSLLLERLQEEFEKGL 85 (200)
T ss_pred HHHHHHHHHHHHHHHccCHHHHHHHHHHH-HHH------HHcCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345666666666666553 3556789999 999 9999999999999999999988878777777777777552
Q ss_pred hcccccccccchhhhhhhhhhcchhhhhhhhccccccchhhHHhhHHHHHHHHHhhCccccc-ccccee
Q psy7791 447 HRLDINKLRDDVCVINVVVKINGLTRLQFLYLSSNVVSNYDKLRNVAKFFAHQLFTDAIGWH-VLSCIH 514 (551)
Q Consensus 447 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~Nlak~~a~Ll~~~~l~l~-vLk~i~ 514 (551)
+..+.. ..+|..++.+|+|+|+..+.++-. ++.+++
T Consensus 86 e~~~~~--------------------------------~~~~~~~~i~fl~eL~~~~~i~~~~i~~~l~ 122 (200)
T smart00543 86 ESEEES--------------------------------DKQRRLGLVRFLGELYNFQVLTSKIILELLK 122 (200)
T ss_pred HHHHHH--------------------------------hhhhHHhHHHHHHHHHHcccCcHHHHHHHHH
Confidence 221111 145699999999999999999764 555554
No 13
>KOG2412|consensus
Probab=92.58 E-value=3.9 Score=45.52 Aligned_cols=189 Identities=16% Similarity=0.207 Sum_probs=114.1
Q ss_pred hHHHHHHHHhHHhhhcCCCc---HHHHHHHHHHHH---hhhh----h----hHHHHHHHHHH----hcCCchHHHHHHHH
Q psy7791 53 SWETLKKSIHGSVNKVNTGN---IGIIARKLFQEN---IIRG----R----GLLTRTILQAQ----AASPTFTNVYAALV 114 (551)
Q Consensus 53 ~w~~L~r~I~glLNKLs~~N---i~~i~~eL~~~n---~~~g----r----~ll~~~Il~~~----~~~~~~~~vyAaLi 114 (551)
.-..++|.|+--++-+|.+| |..|..+|.+.- +..+ . ..++.+++... +..|.=.--.|.+|
T Consensus 334 ~~~~~kr~in~~~~qis~~~~q~L~qI~dkl~s~~~~~~~~~~pl~~~~~~~~iaka~V~Q~Etev~~~PeaAfPla~V~ 413 (591)
T KOG2412|consen 334 YNQSLKRAINPPFSQISKSNGQVLRQIFDKLDSLFGGIPDIVDPLAYDWCLNFIAKAFVKQAETEVASKPEAAFPLAKVI 413 (591)
T ss_pred HHHHHHhhcCCChhhhhhccHHHHHHHHHHHHHHhcCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHhCCcccchHHHHH
Confidence 34577888887777777666 444555554432 1111 1 23555555432 22342222367788
Q ss_pred HHHHccCCchHHHHHHHHHHH---------------HHH--HHhccCc----------cchhhHHHHHHHHHhccc----
Q psy7791 115 DIINSKFPSIGELLLNRCIQQ---------------FKR--SFKRNDK----------ALCINSVTFIAHLVNQQV---- 163 (551)
Q Consensus 115 a~L~~~~pevG~~ll~~lv~~---------------F~~--~~~~~d~----------k~~~n~~~fia~Lynf~V---- 163 (551)
..|...+|+||.+|+.++.++ +.+ +|+..|+ ++..+++++.|-+...+.
T Consensus 414 l~i~~q~Pdv~dlllA~l~KkCP~~VPf~~~~~~Eq~~k~mGyk~~d~nk~Eqnd~YleRm~Gi~rLYAAIi~l~~p~~~ 493 (591)
T KOG2412|consen 414 LYIWSQFPDVGDLLLARLHKKCPYVVPFHIVNSTEQYQKMMGYKAWDSNKWEQNDAYLERMDGIMRLYAAIIQLDIPVGN 493 (591)
T ss_pred HHHHHhCchHHHHHHHHHHhcCCccccccccCcHHHHHHhhcccccccccccccchHHHHhHhHHHHHHHHHHhcccccC
Confidence 889999999999999998653 221 3444443 578888888887776655
Q ss_pred ---ccHH---HHHHHHHHHhcCCCC--CcHHHHHHHHHHhhhhhhcccCccccchhhhcchHHHHHHHHHHHhhhcCCCc
Q psy7791 164 ---AHEI---IVLEILTLLVETPTN--DSDFSLEPYSKHKLHHLRSLMCMPLWWISSIQSFQALESFFSTDVYNSSKGKL 235 (551)
Q Consensus 164 ---v~~~---li~dii~~Lle~~te--~~iEll~~lL~~~G~~LR~~dG~~L~~~~~~q~~~~l~~i~~~lr~~l~~~~~ 235 (551)
+|+- .-...+..++..+-. -..-++..+|.+||+.|-..=|.+..... --.-+.++.+++..-+.|.
T Consensus 494 ~~~~hpf~i~~gW~wLA~iln~~p~~~~tatll~s~Lq~aG~~L~q~Yg~Qf~Kll----i~i~E~y~~r~~a~~~~g~- 568 (591)
T KOG2412|consen 494 ATNVHPFGINHGWAWLARILNKIPLLDTTATLLNSFLQTAGFGLLQRYGSQFLKLL----ILIREHYLPRLAAKKDTGD- 568 (591)
T ss_pred CCCCCcchhhcccHHHHHHhCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHhhccccccc-
Confidence 3321 223344455554322 23445566999999888777777766654 2233556666665544343
Q ss_pred hhHHHHHHHHHH
Q psy7791 236 EKRVQYMIEVLA 247 (551)
Q Consensus 236 ssR~~fmie~l~ 247 (551)
.|++-.++..+
T Consensus 569 -~rl~ill~~~l 579 (591)
T KOG2412|consen 569 -LRLRILLEAWL 579 (591)
T ss_pred -hHHHHHHHHHH
Confidence 79998888887
No 14
>KOG3942|consensus
Probab=91.63 E-value=0.65 Score=48.12 Aligned_cols=122 Identities=11% Similarity=0.059 Sum_probs=80.3
Q ss_pred CchHHHHHHHHHHHHHHHHhc------cCccchhhHHHHHHHHHhcc-----cccHHHHHHHHHHHhcCCC--CCcHHHH
Q psy7791 122 PSIGELLLNRCIQQFKRSFKR------NDKALCINSVTFIAHLVNQQ-----VAHEIIVLEILTLLVETPT--NDSDFSL 188 (551)
Q Consensus 122 pevG~~ll~~lv~~F~~~~~~------~d~k~~~n~~~fia~Lynf~-----Vv~~~li~dii~~Lle~~t--e~~iEll 188 (551)
+..|..|+..++...++.|.- .+...+...+.|+++||-.= ++=-.+++.|++.++..|. +..+|++
T Consensus 199 ~~~gt~f~~~Lln~lrq~f~~r~gl~s~~~~rw~~fisfltelf~nlgs~p~~vL~~~l~~cl~~llrspd~~~~e~ecl 278 (348)
T KOG3942|consen 199 WRNGTQFMDELLNLLRQGFLLRTGLSSLASCRWWRFISFLTELFDNLGSCPQVVLQRSLRLCLQILLRSPDWPEFEYECL 278 (348)
T ss_pred hhccchHHHHHHHHHHHhhccchhccchhHHHHHHHHHHHHHHHhhcCCCChhhHHHHHHHHHHHHccCCCcchHHHHHH
Confidence 445555666666666666643 24567899999999999653 3444588999999998765 4577777
Q ss_pred HHHHHHhhhhhhcccCccccchhhhcchHHHHHHHHHHHhhh-cCCCchhHHHHHHHHHHHHHHcCCc
Q psy7791 189 EPYSKHKLHHLRSLMCMPLWWISSIQSFQALESFFSTDVYNS-SKGKLEKRVQYMIEVLAQVRKDNFK 255 (551)
Q Consensus 189 ~~lL~~~G~~LR~~dG~~L~~~~~~q~~~~l~~i~~~lr~~l-~~~~~ssR~~fmie~l~dLr~n~~k 255 (551)
.-.|... |..|.+.- |..+...|.-.|+.+ ..++--.-.|-|+=.+..|..+.|+
T Consensus 279 ~~~L~~~--------g~dle~ql----P~ql~lL~~s~rDafL~~sep~a~~r~~lllliel~As~wq 334 (348)
T KOG3942|consen 279 SMKLAVE--------GLDLEKQL----PFQLLLLFPSRRDAFLVRSEPLAPWRCPLLLLIELPASAWQ 334 (348)
T ss_pred HHHHHHc--------Cccchhhh----hHHHHHHHHHHHHhhhccccccccccchhhhccccCccccC
Confidence 6688877 77777765 666666666555553 2222223335566666667777765
No 15
>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=88.82 E-value=3.2 Score=40.59 Aligned_cols=88 Identities=16% Similarity=0.303 Sum_probs=66.4
Q ss_pred hhHHHHHHHHhhcc-hhhHHHHHHHHHHHhhhhhcccccccccchhhhhhhhhhcchhhhhhhhccccccchhhHHhhHH
Q psy7791 415 KFFGLLAQRFCQIN-KMYVAPLEQIFRESYSTVHRLDINKLRDDVCVINVVVKINGLTRLQFLYLSSNVVSNYDKLRNVA 493 (551)
Q Consensus 415 pyY~~la~rlC~~~-~~~~~tfq~~fwd~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~Nla 493 (551)
=||+.|.-.||+.. ..+-..|..++.-.|+.++.++..- ...++
T Consensus 90 iyY~sllielCk~~P~~i~pv~~~air~ly~~l~~md~e~-----------------------------------~~Rf~ 134 (191)
T PF09088_consen 90 IYYHSLLIELCKLSPSAIPPVLGRAIRFLYRNLDSMDFEL-----------------------------------RDRFV 134 (191)
T ss_dssp HHHHHHHHHHHHHSTTTHHHHHHHHHHHHHHGGGGB-HHH-----------------------------------HHHHH
T ss_pred hHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHhhhhcCHHH-----------------------------------HHHHH
Confidence 38999999999987 4688999999999999999988643 77888
Q ss_pred HHHHHHHhhCccccccccceecCccccCcchHHHHHHHHHHHHH
Q psy7791 494 KFFAHQLFTDAIGWHVLSCIHLNEEETTSSGRIFIKILFQELSE 537 (551)
Q Consensus 494 k~~a~Ll~~~~l~l~vLk~i~~~e~~t~~~~riF~k~Lf~el~~ 537 (551)
-.|+|-++.-...|.==..++-.+.+...+.++|++-++.-.+-
T Consensus 135 dWfS~hLSNF~f~W~W~eW~~~~~l~~~~pk~~Fi~~~l~k~iR 178 (191)
T PF09088_consen 135 DWFSHHLSNFGFQWKWDEWVDDLELPPLHPKRVFIREVLEKEIR 178 (191)
T ss_dssp HHHHHHHHTTTT---GGGGGGGTTS-TTSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhcCCceeeHHHhhhhhhCCccCCHHHHHHHHHHHHHh
Confidence 99999998887766433445545666667789999998876553
No 16
>PF07817 GLE1: GLE1-like protein; InterPro: IPR012476 The members of this family are sequences that are similar to the human protein GLE1 (O75458 from SWISSPROT). This protein is localised at the nuclear pore complexes and functions in poly(A)+ RNA export to the cytoplasm []. ; GO: 0016973 poly(A)+ mRNA export from nucleus, 0005643 nuclear pore; PDB: 3PEV_B 3RRN_B 3PEU_B 3RRM_B.
Probab=82.89 E-value=7.4 Score=39.68 Aligned_cols=83 Identities=19% Similarity=0.253 Sum_probs=54.0
Q ss_pred HhhHHHHHHHHhHHhhhcCCCcHHHH---HHHHHHH----------Hhh--h----h----hhHHHHHHHHHH----hcC
Q psy7791 51 RISWETLKKSIHGSVNKVNTGNIGII---ARKLFQE----------NII--R----G----RGLLTRTILQAQ----AAS 103 (551)
Q Consensus 51 ~~~w~~L~r~I~glLNKLs~~Ni~~i---~~eL~~~----------n~~--~----g----r~ll~~~Il~~~----~~~ 103 (551)
+..+..++|.|+.-+|.||.++ ..| +.+|.+. -.. . + -..+++.|+... ...
T Consensus 23 Kk~~~~~kr~I~~~vgQls~~~-~qi~~i~~~i~~ll~~~~~~~~~~~~~~~~~~~~~~~~l~~lAk~iv~Q~e~ev~~~ 101 (256)
T PF07817_consen 23 KKLRFDLKRKINPKVGQLSNSS-SQINRIINQISNLLSGQPVKSNDLQQSKNDHPLAYKYLLNFLAKKIVSQAETEVSAN 101 (256)
T ss_dssp HHHHHHHHHHHCCHHHC--SBH-HHHHHHHHHHHHH----------HHTTTT-SHHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHhhhhCcCcHhhccCcH-HHHHHHHHHHHHHhhhhhhchhhhhhhccCCchHHHHHHHHHHHHHHHHHHHHhccC
Confidence 3457899999999999999987 444 3455544 110 1 1 124566666442 124
Q ss_pred CchHHHHHHHHHHHHccCCchHHHHHHHHHH
Q psy7791 104 PTFTNVYAALVDIINSKFPSIGELLLNRCIQ 134 (551)
Q Consensus 104 ~~~~~vyAaLia~L~~~~pevG~~ll~~lv~ 134 (551)
|...-.+|.+++.|-...|++|..|+.++..
T Consensus 102 ~~~A~PlA~v~~~l~~~~p~~~dillA~l~k 132 (256)
T PF07817_consen 102 PESAFPLARVAVQLWSQHPEFGDILLARLHK 132 (256)
T ss_dssp GGGHHHHHHHHHHHHHHSTCHHHHHHHHHHH
T ss_pred CchhhhHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence 6666678999999999999999988877653
No 17
>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=71.20 E-value=18 Score=31.36 Aligned_cols=104 Identities=12% Similarity=0.165 Sum_probs=60.1
Q ss_pred HHHHhHHhh-hcCCCcHHHHHHHHHHHHhhhhhhHHHHHHHHHHhcC-CchHHHHHHHHHHHHccCCchHHHHHHHHHHH
Q psy7791 58 KKSIHGSVN-KVNTGNIGIIARKLFQENIIRGRGLLTRTILQAQAAS-PTFTNVYAALVDIINSKFPSIGELLLNRCIQQ 135 (551)
Q Consensus 58 ~r~I~glLN-KLs~~Ni~~i~~eL~~~n~~~gr~ll~~~Il~~~~~~-~~~~~vyAaLia~L~~~~pevG~~ll~~lv~~ 135 (551)
||+++.+|. =++..+....+..|-+.+.......++..++...... +..-+.|+.|.+.+...-.- .-+.+..-
T Consensus 2 rk~i~~~l~ey~~~~d~~ea~~~l~el~~~~~~~~vv~~~l~~~le~~~~~r~~~~~Ll~~L~~~~~~----~~~~~~~g 77 (113)
T PF02847_consen 2 RKKIFSILMEYFSSGDVDEAVECLKELKLPSQHHEVVKVILECALEEKKSYREYYSKLLSHLCKRKLI----SKEQFQEG 77 (113)
T ss_dssp HHHHHHHHHHHHHHT-HHHHHHHHHHTT-GGGHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHTTSS-----HHHHHHH
T ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHhCCCccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHhcCCC----CHHHHHHH
Confidence 455555444 2333566667777766665544556777777776655 66778888888888743211 11112222
Q ss_pred HHHHHhc------cCccchhhHHHHHHHHHhccccc
Q psy7791 136 FKRSFKR------NDKALCINSVTFIAHLVNQQVAH 165 (551)
Q Consensus 136 F~~~~~~------~d~k~~~n~~~fia~Lynf~Vv~ 165 (551)
|..-+.. .-.+...++..|+++++.-++++
T Consensus 78 f~~~l~~l~Dl~~D~P~~~~~la~~~~~~i~~~~lp 113 (113)
T PF02847_consen 78 FEDLLESLEDLELDIPKAPEYLAKFLARLIADGILP 113 (113)
T ss_dssp HHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTSS-
T ss_pred HHHHHhHhhhccccchHHHHHHHHHHHHHHHcCCcC
Confidence 2222221 12567888999999999888763
No 18
>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=63.09 E-value=61 Score=28.10 Aligned_cols=104 Identities=15% Similarity=0.226 Sum_probs=62.7
Q ss_pred HHHHhHHhhh-cCCCcHHHHHHHHHHHHhhhhhhHHHHHHHHHHhcC-CchHHHHHHHHHHHHccCCchHHHHHHHHHHH
Q psy7791 58 KKSIHGSVNK-VNTGNIGIIARKLFQENIIRGRGLLTRTILQAQAAS-PTFTNVYAALVDIINSKFPSIGELLLNRCIQQ 135 (551)
Q Consensus 58 ~r~I~glLNK-Ls~~Ni~~i~~eL~~~n~~~gr~ll~~~Il~~~~~~-~~~~~vyAaLia~L~~~~pevG~~ll~~lv~~ 135 (551)
||+|..+++. ++.......+..+..++...-...+++.++...... +..-+.|+.|...|...-.--. ..+..-
T Consensus 2 ~k~i~~~l~ey~~~~D~~ea~~~l~~L~~~~~~~~vv~~~i~~~le~~~~~~~~~~~Ll~~L~~~~~~~~----~~~~~~ 77 (113)
T smart00544 2 KKKIFLIIEEYLSSGDTDEAVHCLLELKLPEQHHEVVKVLLTCALEEKRTYREMYSVLLSRLCQANVIST----KQFEKG 77 (113)
T ss_pred hhHHHHHHHHHHHcCCHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHcCCcCH----HHHHHH
Confidence 3444444432 334567777777777776533455666777665555 5788889999998884432111 222333
Q ss_pred HHHHHhcc-----C-ccchhhHHHHHHHHHhccccc
Q psy7791 136 FKRSFKRN-----D-KALCINSVTFIAHLVNQQVAH 165 (551)
Q Consensus 136 F~~~~~~~-----d-~k~~~n~~~fia~Lynf~Vv~ 165 (551)
|..-+..- | .+...++..|+|++.--++++
T Consensus 78 f~~~~~~l~dl~~D~P~a~~~la~~~a~~v~~~~l~ 113 (113)
T smart00544 78 FWRLLEDIEDLELDIPNAWRNLAEFVARLISDGILP 113 (113)
T ss_pred HHHHHhhChhhhcccccHHHHHHHHHHHHHHcCCCC
Confidence 33333331 2 367888999999998877763
No 19
>PF15359 CDV3: Carnitine deficiency-associated protein 3
Probab=62.11 E-value=4.8 Score=36.95 Aligned_cols=18 Identities=33% Similarity=0.514 Sum_probs=13.2
Q ss_pred cCCCCCCcccChHHhhhh
Q psy7791 20 LSSKTGGAYIPPAKLKLM 37 (551)
Q Consensus 20 ~~~~~~~kYVPP~~~r~~ 37 (551)
....++|+||||++|...
T Consensus 81 ~p~~~~gvY~PP~~R~~~ 98 (129)
T PF15359_consen 81 EPATTSGVYRPPAARNTT 98 (129)
T ss_pred CCCCCCceecCccccccc
Confidence 335689999999965443
No 20
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=60.62 E-value=55 Score=30.37 Aligned_cols=99 Identities=12% Similarity=0.093 Sum_probs=64.2
Q ss_pred hhhHHHHHHHHHhcccccHHHHHHHHHHHhcCCCCC----cHHHHHHHHHHhhhhhhcccCccccchhhhcchHHHHHHH
Q psy7791 148 CINSVTFIAHLVNQQVAHEIIVLEILTLLVETPTND----SDFSLEPYSKHKLHHLRSLMCMPLWWISSIQSFQALESFF 223 (551)
Q Consensus 148 ~~n~~~fia~Lynf~Vv~~~li~dii~~Lle~~te~----~iEll~~lL~~~G~~LR~~dG~~L~~~~~~q~~~~l~~i~ 223 (551)
=..++.-||.+.|-+-..+......|+.-+.+.+.. .+.++-.++++| |..+...+ +-+.++
T Consensus 18 dw~~ileicD~In~~~~~~k~a~rai~krl~~~n~~v~l~AL~LLe~~vkNC--------G~~fh~ev------as~~Fl 83 (139)
T cd03567 18 DWEAIQAFCEQINKEPEGPQLAVRLLAHKIQSPQEKEALQALTVLEACMKNC--------GERFHSEV------GKFRFL 83 (139)
T ss_pred CHHHHHHHHHHHHcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHc--------CHHHHHHH------HhHHHH
Confidence 344567788888888777777777777777766654 344445566677 77776643 334455
Q ss_pred HHHHhhhc----CCCchhHHHHHHHHHHHHHHcCCcCCCCc
Q psy7791 224 STDVYNSS----KGKLEKRVQYMIEVLAQVRKDNFKDFPDV 260 (551)
Q Consensus 224 ~~lr~~l~----~~~~ssR~~fmie~l~dLr~n~~k~~~~~ 260 (551)
+.+.+++. ++..+.+++-.+-.++.--...|++.|.+
T Consensus 84 ~el~kl~~~k~~~~~~~~~Vk~kil~li~~W~~~f~~~p~~ 124 (139)
T cd03567 84 NELIKLVSPKYLGSRTSEKVKTKIIELLYSWTLELPHEPKI 124 (139)
T ss_pred HHHHHHhccccCCCCCCHHHHHHHHHHHHHHHHHhcccchH
Confidence 55555553 24567788877777777666677766654
No 21
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=52.33 E-value=1.1e+02 Score=28.58 Aligned_cols=95 Identities=11% Similarity=0.023 Sum_probs=59.7
Q ss_pred hhHHHHHHHHHhcccccHHHHHHHHHHHhcCCCCC----cHHHHHHHHHHhhhhhhcccCccccchhhhcchHHHHHHHH
Q psy7791 149 INSVTFIAHLVNQQVAHEIIVLEILTLLVETPTND----SDFSLEPYSKHKLHHLRSLMCMPLWWISSIQSFQALESFFS 224 (551)
Q Consensus 149 ~n~~~fia~Lynf~Vv~~~li~dii~~Lle~~te~----~iEll~~lL~~~G~~LR~~dG~~L~~~~~~q~~~~l~~i~~ 224 (551)
..++.=||.+.|.+-..++-+...|+.=+.+.+.. .+.++-.++++| |..+...+ +-+.+.+
T Consensus 18 w~~il~icD~I~~~~~~~k~a~ral~KRl~~~n~~v~l~AL~LLe~~vkNC--------G~~fh~ev------ask~Fl~ 83 (144)
T cd03568 18 WGLILDVCDKVKSDENGAKDCLKAIMKRLNHKDPNVQLRALTLLDACAENC--------GKRFHQEV------ASRDFTQ 83 (144)
T ss_pred HHHHHHHHHHHhcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHC--------CHHHHHHH------hhHHHHH
Confidence 34667789999988888888877777777665554 445555566677 87777633 3456677
Q ss_pred HHHhhhcCCCchhHHHHHHHHHHHHHHcCCcCCC
Q psy7791 225 TDVYNSSKGKLEKRVQYMIEVLAQVRKDNFKDFP 258 (551)
Q Consensus 225 ~lr~~l~~~~~ssR~~fmie~l~dLr~n~~k~~~ 258 (551)
.|.+++... ....++-.+-.++.--...|++.|
T Consensus 84 eL~kl~~~~-~~~~Vk~kil~li~~W~~~f~~~~ 116 (144)
T cd03568 84 ELKKLINDR-VHPTVKEKLREVVKQWADEFKNDP 116 (144)
T ss_pred HHHHHhccc-CCHHHHHHHHHHHHHHHHHhCCCc
Confidence 777777553 455555444444444444554433
No 22
>PF09733 VEFS-Box: VEFS-Box of polycomb protein; InterPro: IPR019135 The VEFS-Box is found in the the C-terminal region of the VRN2, EMF2, FIS2, and Su(z)12 polycomb proteins. This domain is characterised by an acidic cluster and a tryptophan/methionine-rich sequence, the acidic-W/M domain []. In some proteins the VEFS-Box is associated with a zinc-finger domain located roughly 100 residues towards the N terminus. These proteins are part of the polycomb cluster of proteins which control HOX gene transcription as it functions in heterochromatin-mediated repression [].
Probab=52.17 E-value=30 Score=32.22 Aligned_cols=31 Identities=13% Similarity=0.111 Sum_probs=27.4
Q ss_pred cchhhHHHHHHHHHhcccccHHHHHHHHHHH
Q psy7791 146 ALCINSVTFIAHLVNQQVAHEIIVLEILTLL 176 (551)
Q Consensus 146 k~~~n~~~fia~Lynf~Vv~~~li~dii~~L 176 (551)
..+.|.+.+++.|+++|+++...|.+|++.|
T Consensus 110 ~l~~~f~lHl~~L~d~glLd~~~i~~c~~~l 140 (140)
T PF09733_consen 110 NLRREFLLHLINLWDFGLLDARTIDECMKIL 140 (140)
T ss_pred hHHHHHHHHHHHHHHcCCCCHHHHHHHHhhC
Confidence 4577788999999999999999999999865
No 23
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=49.20 E-value=1.4e+02 Score=27.68 Aligned_cols=96 Identities=15% Similarity=0.069 Sum_probs=60.8
Q ss_pred hhhHHHHHHHHHhcccccHHHHHHHHHHHhcCCCCC----cHHHHHHHHHHhhhhhhcccCccccchhhhcchHHHHHHH
Q psy7791 148 CINSVTFIAHLVNQQVAHEIIVLEILTLLVETPTND----SDFSLEPYSKHKLHHLRSLMCMPLWWISSIQSFQALESFF 223 (551)
Q Consensus 148 ~~n~~~fia~Lynf~Vv~~~li~dii~~Lle~~te~----~iEll~~lL~~~G~~LR~~dG~~L~~~~~~q~~~~l~~i~ 223 (551)
=...+.-||.+.|-+-..+.-+...|+.=+...+.. .+.++-.++++| |..+.... +-+...
T Consensus 21 dw~~ileicD~In~~~~~~k~a~ral~krl~~~n~~vql~AL~LLe~~vkNC--------G~~fh~ev------as~~fl 86 (142)
T cd03569 21 DLASILEICDMIRSKDVQPKYAMRALKKRLLSKNPNVQLYALLLLESCVKNC--------GTHFHDEV------ASREFM 86 (142)
T ss_pred CHHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHC--------CHHHHHHH------hhHHHH
Confidence 445677788999988788888888777777665544 455555667777 77777643 345677
Q ss_pred HHHHhhhcCCCchhHHHHHHHHHHHHHHcCCcCCC
Q psy7791 224 STDVYNSSKGKLEKRVQYMIEVLAQVRKDNFKDFP 258 (551)
Q Consensus 224 ~~lr~~l~~~~~ssR~~fmie~l~dLr~n~~k~~~ 258 (551)
+.|.+++.. ..+.+++-.+-.++.--...|++.|
T Consensus 87 ~~l~~l~~~-~~~~~Vk~kil~li~~W~~~f~~~~ 120 (142)
T cd03569 87 DELKDLIKT-TKNEEVRQKILELIQAWALAFRNKP 120 (142)
T ss_pred HHHHHHHcc-cCCHHHHHHHHHHHHHHHHHhCCCc
Confidence 777777754 5566665443333333334554433
No 24
>KOG2297|consensus
Probab=49.11 E-value=51 Score=34.85 Aligned_cols=60 Identities=17% Similarity=0.113 Sum_probs=45.9
Q ss_pred HhhHHHHHHHHHhhCccccccccceecCccccCcchHHHHHHHHHHHHHHhcHHHHhhhh
Q psy7791 489 LRNVAKFFAHQLFTDAIGWHVLSCIHLNEEETTSSGRIFIKILFQELSEYMGLSKLNQKI 548 (551)
Q Consensus 489 l~Nlak~~a~Ll~~~~l~l~vLk~i~~~e~~t~~~~riF~k~Lf~el~~~lg~~~l~~~l 548 (551)
-.-||.|-|-|++.|.+|-+||..+.=..+-..-..--|.--||++...+=||..|-.-|
T Consensus 147 r~KLA~~Tal~l~nGt~~~tvl~~L~~d~LVkeGi~l~F~~~lFk~~~~Ek~i~~lis~L 206 (412)
T KOG2297|consen 147 RKKLAMLTALLLSNGTLPATVLQSLLNDNLVKEGIALSFAVKLFKEWLVEKDINDLISSL 206 (412)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHhhHHHHhHHHHHHHHHHHHHHhhccHHHHHHHH
Confidence 678999999999999999999988743333222234678888999999998888765433
No 25
>KOG2140|consensus
Probab=48.40 E-value=90 Score=35.28 Aligned_cols=110 Identities=19% Similarity=0.255 Sum_probs=62.1
Q ss_pred HHHHHHHHhHHhhhcCCCcHHHHHHHHHHHHhhhhh-hHHHHHHHHHHhcCCchHHHHHHHHHHHHccCCchHHHHHHHH
Q psy7791 54 WETLKKSIHGSVNKVNTGNIGIIARKLFQENIIRGR-GLLTRTILQAQAASPTFTNVYAALVDIINSKFPSIGELLLNRC 132 (551)
Q Consensus 54 w~~L~r~I~glLNKLs~~Ni~~i~~eL~~~n~~~gr-~ll~~~Il~~~~~~~~~~~vyAaLia~L~~~~pevG~~ll~~l 132 (551)
...+||.|-=.+ -|.--++..+++|+..-+..|. .-||.-|+..+....+|...|.-|.-.... |-..-
T Consensus 451 lv~frr~IYLti--~SSldfeEaaHKLLKmkip~~q~~elc~mii~cc~QerTy~kFYglL~eRfc~--------l~r~~ 520 (739)
T KOG2140|consen 451 LVNFRRTIYLTI--QSSLDFEEAAHKLLKMKIPESQEKELCNMIIDCCAQERTYEKFYGLLGERFCM--------LHREW 520 (739)
T ss_pred hHHhhhhheeee--eccCcHHHHHHHHHhccCCchhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH--------HHHHH
Confidence 345555554222 1233456666778777766663 457888888766667777767554222110 00111
Q ss_pred HHHHHH----HHh---ccCccchhhHHHHHHHHHhcccccHHHHHHHHH
Q psy7791 133 IQQFKR----SFK---RNDKALCINSVTFIAHLVNQQVAHEIIVLEILT 174 (551)
Q Consensus 133 v~~F~~----~~~---~~d~k~~~n~~~fia~Lynf~Vv~~~li~dii~ 174 (551)
+..|++ .|. +-+....-|+.+|+|||.....++= =++.||+
T Consensus 521 q~~fe~~f~q~YstIhr~EtnkLRnlakffahLlstd~lpw-~vl~~ik 568 (739)
T KOG2140|consen 521 QEAFEKCFKQQYSTIHRYETNKLRNLAKFFAHLLSTDALPW-DVLACIK 568 (739)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcccccch-HHHHHhh
Confidence 122222 221 2245568999999999998887774 3455555
No 26
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=44.60 E-value=1.7e+02 Score=26.48 Aligned_cols=94 Identities=14% Similarity=0.034 Sum_probs=62.0
Q ss_pred hhHHHHHHHHHhcccccHHHHHHHHHHHhcCCCCC----cHHHHHHHHHHhhhhhhcccCccccchhhhcchHHHHHHHH
Q psy7791 149 INSVTFIAHLVNQQVAHEIIVLEILTLLVETPTND----SDFSLEPYSKHKLHHLRSLMCMPLWWISSIQSFQALESFFS 224 (551)
Q Consensus 149 ~n~~~fia~Lynf~Vv~~~li~dii~~Lle~~te~----~iEll~~lL~~~G~~LR~~dG~~L~~~~~~q~~~~l~~i~~ 224 (551)
..++.-||.+.|.+-.++..+...|+.-+...+.. .+.++-.++++| |..+.... +-+..++
T Consensus 18 ~~~il~icd~I~~~~~~~k~a~raL~krl~~~n~~vql~AL~lLd~~vkNc--------g~~f~~~i------~s~~fl~ 83 (133)
T cd03561 18 WALNLELCDLINLKPNGPKEAARAIRKKIKYGNPHVQLLALTLLELLVKNC--------GKPFHLQV------ADKEFLL 83 (133)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhC--------ChHHHHHH------hhHHHHH
Confidence 45678899999999999999999999888876654 455555566777 77666533 2244555
Q ss_pred HHHhhhcCC-CchhHHHHHHHHHHHHHHcCCcC
Q psy7791 225 TDVYNSSKG-KLEKRVQYMIEVLAQVRKDNFKD 256 (551)
Q Consensus 225 ~lr~~l~~~-~~ssR~~fmie~l~dLr~n~~k~ 256 (551)
.+.+++... ..+..++-.+-.++.--...++.
T Consensus 84 ~l~~l~~~~~~~~~~Vk~kil~ll~~W~~~f~~ 116 (133)
T cd03561 84 ELVKIAKNSPKYDPKVREKALELILAWSESFGG 116 (133)
T ss_pred HHHHHhCCCCCCCHHHHHHHHHHHHHHHHHhcC
Confidence 666666553 56777765554444444445543
No 27
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=44.21 E-value=1.9e+02 Score=26.29 Aligned_cols=71 Identities=13% Similarity=0.010 Sum_probs=49.3
Q ss_pred hhhHHHHHHHHHhcccccHHHHHHHHHHHhcCCCCC----cHHHHHHHHHHhhhhhhcccCccccchhhhcchHHHHHHH
Q psy7791 148 CINSVTFIAHLVNQQVAHEIIVLEILTLLVETPTND----SDFSLEPYSKHKLHHLRSLMCMPLWWISSIQSFQALESFF 223 (551)
Q Consensus 148 ~~n~~~fia~Lynf~Vv~~~li~dii~~Lle~~te~----~iEll~~lL~~~G~~LR~~dG~~L~~~~~~q~~~~l~~i~ 223 (551)
=...+.-||.+.|.+-.++..+...|+.=+...+.. .+.++=.++++| |..+.... +-+...
T Consensus 17 dw~~~l~icD~i~~~~~~~k~a~r~l~krl~~~n~~v~l~AL~lLe~~vkNc--------g~~f~~ev------~s~~fl 82 (133)
T smart00288 17 DWELILEICDLINSTPDGPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNC--------GSKFHLEV------ASKEFL 82 (133)
T ss_pred CHHHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHC--------CHHHHHHH------HhHHHH
Confidence 344677889999999888898888888877776655 455555566777 77776533 334556
Q ss_pred HHHHhhhcC
Q psy7791 224 STDVYNSSK 232 (551)
Q Consensus 224 ~~lr~~l~~ 232 (551)
+.|..++..
T Consensus 83 ~~L~~l~~~ 91 (133)
T smart00288 83 NELVKLIKP 91 (133)
T ss_pred HHHHHHHcC
Confidence 666666654
No 28
>KOG2188|consensus
Probab=37.79 E-value=2.4e+02 Score=32.54 Aligned_cols=25 Identities=24% Similarity=0.283 Sum_probs=14.9
Q ss_pred HHHHHHHHhcccccHHHHHHHHHHH
Q psy7791 152 VTFIAHLVNQQVAHEIIVLEILTLL 176 (551)
Q Consensus 152 ~~fia~Lynf~Vv~~~li~dii~~L 176 (551)
..++-||++|.--|-.+..+.+.-|
T Consensus 486 a~lle~lv~f~k~~i~~litsll~L 510 (650)
T KOG2188|consen 486 AVLLEELVNFSKTHIQTLITSLLSL 510 (650)
T ss_pred hHHHHHHHhhchhhhHHHHHHHHhh
Confidence 5566777777666655555544444
No 29
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=36.27 E-value=49 Score=29.72 Aligned_cols=38 Identities=13% Similarity=0.201 Sum_probs=27.4
Q ss_pred cccchhhHHHHHHHHhhcchhhHHHHHHHHHHHhhhhhcc
Q psy7791 410 LRTYEKFFGLLAQRFCQINKMYVAPLEQIFRESYSTVHRL 449 (551)
Q Consensus 410 EktyNpyY~~la~rlC~~~~~~~~tfq~~fwd~~~~i~~~ 449 (551)
+.-|+.||..|...++.....- ..|.+|.+.|+....+
T Consensus 2 ~~~~~~y~~~l~~~~~~~~~~~--~~qdvf~~~w~~~~~~ 39 (142)
T TIGR03209 2 EEIYMNFKNTIDIFTRKYNLYY--DYNDILYHLWIILKKI 39 (142)
T ss_pred hHHHHHHHHHHHHHHHHhcchh--hHHHHHHHHHHHHHHh
Confidence 5679999999988888765433 3488888888776543
No 30
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=35.92 E-value=3.5e+02 Score=29.68 Aligned_cols=173 Identities=13% Similarity=0.085 Sum_probs=84.9
Q ss_pred HHHhHHhhhcCCCcHHHHHHHHHHHHhhhh----hhHHHHHHHHHHh-cCCchHHHHHHHHHHHHc--------------
Q psy7791 59 KSIHGSVNKVNTGNIGIIARKLFQENIIRG----RGLLTRTILQAQA-ASPTFTNVYAALVDIINS-------------- 119 (551)
Q Consensus 59 r~I~glLNKLs~~Ni~~i~~eL~~~n~~~g----r~ll~~~Il~~~~-~~~~~~~vyAaLia~L~~-------------- 119 (551)
+.+.-+.+=.++.|+..|+.+|...-...+ +..+++.|..... ..+......-.++..+..
T Consensus 323 ~~l~lL~~l~~~~n~~~Il~eL~~~l~~~~d~~~~~~~i~~I~~la~~~~~~~~~~v~~l~~ll~~~~~~~~~~~~~~i~ 402 (526)
T PF01602_consen 323 KALDLLYKLANESNVKEILDELLKYLSELSDPDFRRELIKAIGDLAEKFPPDAEWYVDTLLKLLEISGDYVSNEIINVIR 402 (526)
T ss_dssp HHHHHHHHH--HHHHHHHHHHHHHHHHHC--HHHHHHHHHHHHHHHHHHGSSHHHHHHHHHHHHHCTGGGCHCHHHHHHH
T ss_pred HHHHHHhhcccccchhhHHHHHHHHHHhccchhhhhhHHHHHHHHHhccCchHHHHHHHHHHhhhhccccccchHHHHHH
Confidence 456666666777999999998876442221 2223333322111 122222222223333332
Q ss_pred ----cCCchHHHHHHHHHHHHHHHHhccCccchhhHHHHHHHHHhcccccHHHHHHHHHHHhcCCCCCcHHHHHHHHHHh
Q psy7791 120 ----KFPSIGELLLNRCIQQFKRSFKRNDKALCINSVTFIAHLVNQQVAHEIIVLEILTLLVETPTNDSDFSLEPYSKHK 195 (551)
Q Consensus 120 ----~~pevG~~ll~~lv~~F~~~~~~~d~k~~~n~~~fia~Lynf~Vv~~~li~dii~~Lle~~te~~iEll~~lL~~~ 195 (551)
..|+..+..+..++..+.. -.+.......+-++|+.-..-.-.. .+.++++.+.+.+.+.+.++=+.++...
T Consensus 403 ~ll~~~~~~~~~~l~~L~~~l~~---~~~~~~~~~~~wilGEy~~~~~~~~-~~~~~~~~l~~~~~~~~~~vk~~ilt~~ 478 (526)
T PF01602_consen 403 DLLSNNPELREKILKKLIELLED---ISSPEALAAAIWILGEYGELIENTE-SAPDILRSLIENFIEESPEVKLQILTAL 478 (526)
T ss_dssp HHHHHSTTTHHHHHHHHHHHHTS---SSSHHHHHHHHHHHHHHCHHHTTTT-HHHHHHHHHHHHHTTSHHHHHHHHHHHH
T ss_pred HHhhcChhhhHHHHHHHHHHHHH---hhHHHHHHHHHhhhcccCCcccccc-cHHHHHHHHHHhhccccHHHHHHHHHHH
Confidence 2344444444444443332 1223334555666666433332224 7888888888888888877777777777
Q ss_pred hhhhhcccCccccchhhhcchHHHHHHHHHHHhhhc--C--CCchhHHHHHHHHH
Q psy7791 196 LHHLRSLMCMPLWWISSIQSFQALESFFSTDVYNSS--K--GKLEKRVQYMIEVL 246 (551)
Q Consensus 196 G~~LR~~dG~~L~~~~~~q~~~~l~~i~~~lr~~l~--~--~~~ssR~~fmie~l 246 (551)
.+-..... .+ ..-+.+++.+..... . -++..|.+|....+
T Consensus 479 --------~Kl~~~~~-~~--~~~~~i~~~~~~~~~~~s~~~evr~Ra~~y~~ll 522 (526)
T PF01602_consen 479 --------AKLFKRNP-EN--EVQNEILQFLLSLATEDSSDPEVRDRAREYLRLL 522 (526)
T ss_dssp --------HHHHHHSC-ST--THHHHHHHHHHCHHHHS-SSHHHHHHHHHHHHHH
T ss_pred --------HHHHhhCC-ch--hhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHH
Confidence 33222221 00 112245555555544 2 35566776665543
No 31
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=30.10 E-value=1.7e+02 Score=26.78 Aligned_cols=95 Identities=18% Similarity=0.078 Sum_probs=55.1
Q ss_pred hHHHHHHHHHhcccccHHHHHHHHHHHhcCCCCC----cHHHHHHHHHHhhhhhhcccCccccchhhhcchHHHHHHHHH
Q psy7791 150 NSVTFIAHLVNQQVAHEIIVLEILTLLVETPTND----SDFSLEPYSKHKLHHLRSLMCMPLWWISSIQSFQALESFFST 225 (551)
Q Consensus 150 n~~~fia~Lynf~Vv~~~li~dii~~Lle~~te~----~iEll~~lL~~~G~~LR~~dG~~L~~~~~~q~~~~l~~i~~~ 225 (551)
..+.-||.+.|-+-..+.-+...|+.=+...+.. .+.++-.++++| |..+.... +-+.+++.
T Consensus 24 ~~~l~icD~i~~~~~~~kea~~~l~krl~~~~~~vq~~aL~lld~lvkNc--------g~~f~~ev------~~~~fl~~ 89 (140)
T PF00790_consen 24 SLILEICDLINSSPDGAKEAARALRKRLKHGNPNVQLLALTLLDALVKNC--------GPRFHREV------ASKEFLDE 89 (140)
T ss_dssp HHHHHHHHHHHTSTTHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHS--------HHHHHHHH------TSHHHHHH
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHcC--------CHHHHHHH------hHHHHHHH
Confidence 3455688899998888888888887777665544 445555567777 65555432 12345566
Q ss_pred HHhhhcCCCchhH--HHHHHHHHHHHHHcCCcCCC
Q psy7791 226 DVYNSSKGKLEKR--VQYMIEVLAQVRKDNFKDFP 258 (551)
Q Consensus 226 lr~~l~~~~~ssR--~~fmie~l~dLr~n~~k~~~ 258 (551)
|.+++........ ++-.+-.++.--...|+..|
T Consensus 90 l~~l~~~~~~~~~~~Vk~k~l~ll~~W~~~f~~~~ 124 (140)
T PF00790_consen 90 LVKLIKSKKTDPETPVKEKILELLQEWAEAFKSDP 124 (140)
T ss_dssp HHHHHHHTTTHHHSHHHHHHHHHHHHHHHHTTTST
T ss_pred HHHHHccCCCCchhHHHHHHHHHHHHHHHHHCCCC
Confidence 6665544333332 65444444444444454433
No 32
>PRK08307 stage III sporulation protein SpoAB; Provisional
Probab=30.04 E-value=72 Score=30.52 Aligned_cols=37 Identities=11% Similarity=0.216 Sum_probs=31.0
Q ss_pred cccchhhHHHHHHHHhhcc-hhhHHHHHHHHHHHhhhh
Q psy7791 410 LRTYEKFFGLLAQRFCQIN-KMYVAPLEQIFRESYSTV 446 (551)
Q Consensus 410 EktyNpyY~~la~rlC~~~-~~~~~tfq~~fwd~~~~i 446 (551)
++.|+.||..+|++|+... .++...++.++++..+..
T Consensus 64 ~~~~~~~f~~~a~~L~~~~g~s~~eaw~~~~~~~~~~~ 101 (171)
T PRK08307 64 PKPISTLFQRFSERLESGEGETAYEAWEKALEENWKNT 101 (171)
T ss_pred chhHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhhcc
Confidence 5679999999999999876 788888888888876554
No 33
>KOG3117|consensus
Probab=29.05 E-value=30 Score=35.90 Aligned_cols=12 Identities=33% Similarity=0.750 Sum_probs=10.1
Q ss_pred CCCCcccChHHh
Q psy7791 23 KTGGAYIPPAKL 34 (551)
Q Consensus 23 ~~~~kYVPP~~~ 34 (551)
+..|+||||-.+
T Consensus 188 ~e~gkYvpPRI~ 199 (340)
T KOG3117|consen 188 AEDGKYVPPRIR 199 (340)
T ss_pred cccCcccCCcee
Confidence 778999999844
No 34
>KOG2229|consensus
Probab=28.01 E-value=6.6e+02 Score=28.58 Aligned_cols=70 Identities=23% Similarity=0.321 Sum_probs=48.6
Q ss_pred hhhhcccCCCHHHHHHHHHccCCCCCCccchheeeeeccccccccccccccchhhHHHHHHHHhhcchhhHHHHHHHHHH
Q psy7791 362 IYLTIHSSLDFEECAHKLLRMQLKPGQESELCHIVHIDTSLWGLFGDQLRTYEKFFGLLAQRFCQINKMYVAPLEQIFRE 441 (551)
Q Consensus 362 If~~ImSS~d~~dA~~kLlkL~lk~~qerEi~~vl~i~C~~~~~~c~qEktyNpyY~~la~rlC~~~~~~~~tfq~~fwd 441 (551)
=|-.|.==-|...=++||++.-+......|+--|+ + -|..||...|+-+-+.| |.|-.
T Consensus 224 nfs~i~ll~DpQ~fAEkLfk~~~~~~er~E~klm~-~--------------------~lisRliG~HkL~l~~f-Y~fl~ 281 (616)
T KOG2229|consen 224 NFSAIHLLHDPQGFAEKLFKQLLACKERFEVKLML-M--------------------KLISRLIGIHKLFLFGF-YPFLQ 281 (616)
T ss_pred CccHHHhhcChhHHHHHHHHHHhhhhhhHHHHHHH-H--------------------HHHHHHhhhhHHHHhhh-HHHHH
Confidence 58888878899999999999766665555655444 3 34678888888888877 45555
Q ss_pred Hhhhhhcccccc
Q psy7791 442 SYSTVHRLDINK 453 (551)
Q Consensus 442 ~~~~i~~~~~~~ 453 (551)
.|-+=|.-++.+
T Consensus 282 ~yl~phqrDvTq 293 (616)
T KOG2229|consen 282 RYLQPHQRDVTQ 293 (616)
T ss_pred HHcCcchhhHHH
Confidence 665555544443
No 35
>TIGR02833 spore_III_AB stage III sporulation protein AB. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage III sporulation protein AB.
Probab=27.62 E-value=62 Score=30.96 Aligned_cols=37 Identities=8% Similarity=0.125 Sum_probs=30.7
Q ss_pred cccchhhHHHHHHHHhhcc-hhhHHHHHHHHHHHhhhh
Q psy7791 410 LRTYEKFFGLLAQRFCQIN-KMYVAPLEQIFRESYSTV 446 (551)
Q Consensus 410 EktyNpyY~~la~rlC~~~-~~~~~tfq~~fwd~~~~i 446 (551)
++.|+.||..+|++|+... .++...++.+++...+..
T Consensus 63 ~~~~~~~f~~~a~~L~~~~g~s~~~~w~~~~~~~~~~~ 100 (170)
T TIGR02833 63 PKPVNLLFESASERLKEGEGLTVYEAWKKALNEVWKQT 100 (170)
T ss_pred chhHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhhcc
Confidence 5679999999999999876 788888888888776543
No 36
>KOG0122|consensus
Probab=25.62 E-value=36 Score=34.57 Aligned_cols=14 Identities=29% Similarity=0.885 Sum_probs=10.9
Q ss_pred CCCCCcccChHHhhh
Q psy7791 22 SKTGGAYIPPAKLKL 36 (551)
Q Consensus 22 ~~~~~kYVPP~~~r~ 36 (551)
....|+||||+ +|.
T Consensus 160 ~~~~g~yvpP~-mR~ 173 (270)
T KOG0122|consen 160 GTKKGKYVPPS-MRA 173 (270)
T ss_pred CCcCccccCcc-ccC
Confidence 45788999999 544
No 37
>KOG1060|consensus
Probab=25.06 E-value=9.4e+02 Score=28.92 Aligned_cols=71 Identities=13% Similarity=0.178 Sum_probs=43.0
Q ss_pred HHHHHHHHHHHhcCCCCCcHHHHHHHHHHhhhhhhcccCccccchhhhcchHHHHHHHHHHHhhhcCCCchhHHHHHHHH
Q psy7791 166 EIIVLEILTLLVETPTNDSDFSLEPYSKHKLHHLRSLMCMPLWWISSIQSFQALESFFSTDVYNSSKGKLEKRVQYMIEV 245 (551)
Q Consensus 166 ~~li~dii~~Lle~~te~~iEll~~lL~~~G~~LR~~dG~~L~~~~~~q~~~~l~~i~~~lr~~l~~~~~ssR~~fmie~ 245 (551)
.+++=|++|.+..+|+.+.-|.=|.+|... .+|---+..|.+.....+|+.-+--+ .=.+-.|.||.=+-
T Consensus 499 pri~PDVLR~laksFs~E~~evKlQILnL~---------aKLyl~~~~~~kll~~Yv~~L~~yD~-sYDiRDRaRF~r~l 568 (968)
T KOG1060|consen 499 PRIAPDVLRKLAKSFSDEGDEVKLQILNLS---------AKLYLTNIDQTKLLVQYVFELARYDL-SYDIRDRARFLRQL 568 (968)
T ss_pred chhchHHHHHHHHhhccccchhhHHHHHhh---------hhheEechhhHHHHHHHHHHHhccCC-CcchhHHHHHHHHH
Confidence 467789999999999999999999999886 33332221222333344444322111 12456677766444
Q ss_pred H
Q psy7791 246 L 246 (551)
Q Consensus 246 l 246 (551)
+
T Consensus 569 ~ 569 (968)
T KOG1060|consen 569 I 569 (968)
T ss_pred h
Confidence 3
No 38
>KOG0482|consensus
Probab=24.08 E-value=5e+02 Score=29.68 Aligned_cols=75 Identities=15% Similarity=-0.013 Sum_probs=48.2
Q ss_pred cccHHHHHHHHHH--------HhcCCCCCcHHHHHHHHHHhhhhhhcccCccccchhhhcchHHHHHHHHHHHhhhcCC-
Q psy7791 163 VAHEIIVLEILTL--------LVETPTNDSDFSLEPYSKHKLHHLRSLMCMPLWWISSIQSFQALESFFSTDVYNSSKG- 233 (551)
Q Consensus 163 Vv~~~li~dii~~--------Lle~~te~~iEll~~lL~~~G~~LR~~dG~~L~~~~~~q~~~~l~~i~~~lr~~l~~~- 233 (551)
-+++..++.||++ |.+...++||+-+++|++-.--.|+.++|+.=+. + +...||..+|+.++++
T Consensus 601 ~ttpRtLL~IlRls~AlarLRls~~V~~~DV~EALRLme~sK~sL~~~~~~~~~~------~-~~~~if~iirel~~e~g 673 (721)
T KOG0482|consen 601 YTTPRTLLGILRLSTALARLRLSDSVEEDDVNEALRLMEMSKDSLYQDDGQKEDT------S-ATDAIFAIIRELAGEGG 673 (721)
T ss_pred ccCHHHHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHhhhccccccccccccc------c-hHHHHHHHHHHHHhhcC
Confidence 3444555555543 2346778999999999999966676666654333 2 3567999999998843
Q ss_pred CchhHHHHHHH
Q psy7791 234 KLEKRVQYMIE 244 (551)
Q Consensus 234 ~~ssR~~fmie 244 (551)
+-..++.-.++
T Consensus 674 ~~~v~~s~~~~ 684 (721)
T KOG0482|consen 674 KRCVKLSNAEQ 684 (721)
T ss_pred CceeeHHHHHH
Confidence 33344444443
No 39
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=21.91 E-value=4.3e+02 Score=21.33 Aligned_cols=73 Identities=21% Similarity=0.276 Sum_probs=41.0
Q ss_pred HHHHHHHHhHHhhhcCCCcHHHHHHHHHHHHhhhhhhHHHHHHHHHHhcCCchHHHHHHHHHHHHccCCchHHHHHHHHH
Q psy7791 54 WETLKKSIHGSVNKVNTGNIGIIARKLFQENIIRGRGLLTRTILQAQAASPTFTNVYAALVDIINSKFPSIGELLLNRCI 133 (551)
Q Consensus 54 w~~L~r~I~glLNKLs~~Ni~~i~~eL~~~n~~~gr~ll~~~Il~~~~~~~~~~~vyAaLia~L~~~~pevG~~ll~~lv 133 (551)
|+.|++.=..++..++ ++..++..|++.+. ++..-++.....++-..--..|+..|-++.+.....|++.+.
T Consensus 1 ~~~L~~~r~~Lv~~l~--~~~~ild~L~~~~v------lt~~e~e~I~~~~t~~~k~~~LLd~l~~kg~~a~~~F~~~L~ 72 (85)
T PF00619_consen 1 QELLRKNRQELVEDLD--DLDDILDHLLSRGV------LTEEEYEEIRSEPTRQDKARKLLDILKRKGPEAFDIFCQALR 72 (85)
T ss_dssp HHHHHHTHHHHHHHSS--HHHHHHHHHHHTTS------SSHHHHHHHHTSSSHHHHHHHHHHHHHHCCHHHHHHHHHHHH
T ss_pred CHHHHHhHHHHHHHhC--cHHHHHHHHHHCCC------CCHHHHHHHHccCChHHHHHHHHHHHHHHCHHHHHHHHHHHH
Confidence 5677777778888888 88888888876544 322222222222332222334555555565555555555444
Q ss_pred H
Q psy7791 134 Q 134 (551)
Q Consensus 134 ~ 134 (551)
.
T Consensus 73 ~ 73 (85)
T PF00619_consen 73 E 73 (85)
T ss_dssp H
T ss_pred h
Confidence 4
Done!