Query 013709
Match_columns 438
No_of_seqs 181 out of 1308
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 06:36:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013709.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013709hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0938 Adaptor complexes medi 100.0 1E-109 2E-114 773.5 40.3 432 4-437 1-446 (446)
2 KOG0937 Adaptor complexes medi 100.0 4.2E-90 9.2E-95 671.4 41.6 421 5-438 1-424 (424)
3 KOG2740 Clathrin-associated pr 100.0 2E-79 4.3E-84 576.3 33.0 409 4-438 1-418 (418)
4 PF00928 Adap_comp_sub: Adapto 100.0 1.1E-61 2.5E-66 467.0 32.6 261 166-438 1-262 (262)
5 KOG2635 Medium subunit of clat 100.0 1.7E-42 3.6E-47 333.8 33.9 398 3-436 1-511 (512)
6 KOG2677 Stoned B synaptic vesi 100.0 1.7E-37 3.6E-42 309.6 9.0 259 173-436 582-889 (922)
7 PF01217 Clat_adaptor_s: Clath 100.0 4.5E-27 9.7E-32 205.1 17.7 135 4-140 1-138 (141)
8 COG5030 APS2 Clathrin adaptor 99.8 6.1E-20 1.3E-24 151.6 12.1 133 4-138 1-136 (152)
9 KOG3343 Vesicle coat complex C 99.8 3.3E-18 7.1E-23 144.5 12.3 140 4-143 8-149 (175)
10 KOG0935 Clathrin adaptor compl 99.7 1.2E-17 2.6E-22 134.2 10.7 134 4-138 1-137 (143)
11 KOG0934 Clathrin adaptor compl 99.7 2.7E-18 5.9E-23 141.8 5.7 127 4-132 1-130 (145)
12 KOG0936 Clathrin adaptor compl 99.7 5.5E-17 1.2E-21 135.8 11.0 134 4-139 1-143 (182)
13 COG5541 RET3 Vesicle coat comp 99.4 3.8E-13 8.3E-18 113.4 9.1 139 4-142 7-155 (187)
14 PF10291 muHD: Muniscin C-term 99.2 1.3E-08 2.8E-13 97.3 23.6 228 180-436 3-256 (257)
15 PF03164 Mon1: Trafficking pro 95.0 0.17 3.8E-06 52.0 10.5 88 6-95 12-102 (415)
16 PF15001 AP-5_subunit_s1: AP-5 94.2 0.28 6.1E-06 44.3 8.5 80 56-136 104-184 (189)
17 COG5122 TRS23 Transport protei 94.0 1.1 2.4E-05 36.7 10.6 93 3-98 1-108 (134)
18 PF08923 MAPKK1_Int: Mitogen-a 93.1 2.3 5.1E-05 35.7 11.7 90 5-95 17-115 (119)
19 PF04099 Sybindin: Sybindin-li 93.1 1.6 3.5E-05 37.9 11.1 91 5-96 1-115 (142)
20 KOG3369 Transport protein part 90.0 3.9 8.4E-05 36.2 9.9 47 50-98 125-172 (199)
21 PF13774 Longin: Regulated-SNA 89.3 2.9 6.2E-05 32.4 8.1 50 48-97 16-65 (83)
22 KOG0997 Uncharacterized conser 88.6 1.8 4E-05 44.3 8.0 86 6-93 118-207 (523)
23 KOG3368 Transport protein part 85.9 9.9 0.00021 32.2 9.5 84 3-90 1-102 (140)
24 KOG0859 Synaptobrevin/VAMP-lik 83.6 30 0.00066 31.5 12.1 85 12-99 8-94 (217)
25 KOG0781 Signal recognition par 82.3 17 0.00037 37.7 11.3 112 4-118 1-116 (587)
26 PF09201 SRX: SRX; InterPro: 73.0 23 0.00049 30.3 7.7 71 4-74 1-86 (148)
27 PF00235 Profilin: Profilin; 47.3 1.6E+02 0.0035 24.2 8.7 87 5-92 16-121 (121)
28 KOG0862 Synaptobrevin/VAMP-lik 46.9 2.4E+02 0.0053 26.2 10.3 49 50-98 53-101 (216)
29 PF04628 Sedlin_N: Sedlin, N-t 37.3 2.5E+02 0.0054 23.7 8.4 90 10-99 1-109 (132)
30 PF08784 RPA_C: Replication pr 33.2 67 0.0015 25.7 4.0 19 110-128 80-98 (102)
31 KOG0861 SNARE protein YKT6, sy 30.4 3.6E+02 0.0079 24.2 8.2 91 3-96 1-102 (198)
32 PF03504 Chlam_OMP6: Chlamydia 28.4 2.9E+02 0.0062 21.6 8.4 43 321-367 43-85 (95)
33 PF13598 DUF4139: Domain of un 27.6 5.7E+02 0.012 24.8 10.4 108 261-377 194-313 (317)
34 PRK09750 hypothetical protein; 24.0 59 0.0013 23.5 1.8 14 415-428 11-24 (64)
35 TIGR01451 B_ant_repeat conserv 23.7 2.6E+02 0.0057 19.5 5.2 31 304-336 12-42 (53)
36 PF07151 DUF1391: Protein of u 21.0 1.1E+02 0.0024 20.6 2.5 17 270-286 16-32 (49)
37 KOG0647 mRNA export protein (c 20.2 2.8E+02 0.006 27.3 6.0 88 185-284 201-291 (347)
No 1
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1e-109 Score=773.46 Aligned_cols=432 Identities=56% Similarity=0.925 Sum_probs=396.9
Q ss_pred eeEEEEEEeCCCCEEEEEcccCCCCCchHHHHHHhhcccccCCCCCeEEECCEEEEEEEeCcEEEEEEEcCCccHHHHHH
Q 013709 4 AASAIYFLNLRGDVLINRLYRDDVGGNMVDAFRTHIMQTKELGTCPVRQIGGCSFFYMRISNVYIVIVVSSNANVACAFK 83 (438)
Q Consensus 4 mI~~i~Il~~~G~~l~~r~y~~~~~~~~~~~f~~~v~~~~~~~~~pi~~~~~~~~~~~~~~~l~~v~~~~~~~n~~~~~~ 83 (438)
||+++||+|.+|++|+.|.||++..++..|+|+-+++.+.+ ..+|+..+++++|+|.+.++||+|++|.+|.|.++++|
T Consensus 1 misglfi~n~rGevlink~fr~dlkrs~~diFRv~vi~n~d-~r~PV~~igsttf~~~r~~nl~lvaitksN~Nva~v~e 79 (446)
T KOG0938|consen 1 MISGLFIYNLRGEVLINKTFRDDLKRSIVDIFRVQVINNLD-VRSPVLTIGSTTFHHIRSSNLWLVAITKSNANVAAVFE 79 (446)
T ss_pred CcceEEEEeccCcEEEehhhhhhhhhhHHHHHHHhhhhccc-cCCCeeEecceeEEEEeeccEEEEEEecCCCchhhHHH
Confidence 89999999999999999999999999999999999998754 79999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhcCCcCCHHHHHhhHHHHHHHHHHHHcCCeecccCHHHHhhhhhccCccCCCCCCCC-CCCCCCCc---
Q 013709 84 FVVEAVALFKSYFGGAFDEDAIRNNFVLIYELLDEIMDFGYPQNLSPEILKLYITQEGVRSPFSSKPT-DRPVPNAT--- 159 (438)
Q Consensus 84 ~L~~~~~vl~~y~~~~l~e~~i~~n~~~i~~lldE~id~G~p~~t~~~~l~~~i~~~~~~~~~~~~~~-~~~~~~~~--- 159 (438)
||..+.+++..|||+ ++|+.|++||.+||||||||+|+||||+|++++|+.+|..++.++..+-... .....+++
T Consensus 80 Fl~kl~avm~aYfgk-~~Eeaiknnf~lI~ElLDemld~G~pqnte~~al~~~is~~~Vrs~g~~ls~k~s~~sq~~~~~ 158 (446)
T KOG0938|consen 80 FLYKLDAVMNAYFGK-DREEAIKNNFVLIYELLDEMLDFGIPQNTEPNALKAQISQKGVRSMGGVLSSKSSPTSQATELR 158 (446)
T ss_pred HHHHHHHHHHHHhcc-cchhhhhhceEeHHHHHHHHHhcCCCccCChhHHHhhhhhhhhhccccccCCcCCCCccccccc
Confidence 999999999999998 9999999999999999999999999999999999999999888765331000 01112232
Q ss_pred -ccccceeecccCCCccccceEEEEEEEeEEEEEecccceEEEEEEEEEEEEEeecCCCeeEEEecCcccccccccc---
Q 013709 160 -LQVTGAVGWRREGLVYKKNEVFLDIVESVNLLMSSKGSVLRCDVTGKILMKCFLSGMPDLKLGLNDKIGLEKESQL--- 235 (438)
Q Consensus 160 -~~~~~~~~WR~~~~~~~~nei~vdV~E~l~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~~~--- 235 (438)
++.+++++||+.|++|+|||+|+||+|++|.+++++|++++++|+|.|.|+|+|||||+|+++|||++.+...+..
T Consensus 159 ssqv~G~i~WRr~Gi~ykknevfldvvErvNlLmS~~GnVLrs~VsG~V~mk~~LSGmPeckfGlNDkl~~e~kq~esks 238 (446)
T KOG0938|consen 159 SSQVTGKIGWRREGIKYKKNEVFLDVVERVNLLMSSDGNVLRSDVSGTVDMKTHLSGMPECKFGLNDKLGMESKQSESKS 238 (446)
T ss_pred ccccccccccccccceeccceeEeEehheeeeEEcCCCCEEEeecccEEEEEEeccCCcccccccCcccceeeccccccc
Confidence 6778999999999999999999999999999999999999999999999999999999999999999876633221
Q ss_pred cC----CCC-CCCceEeeccceeeeeccccCccCcceEEEeCCCCeEEEEEEEecCCCCCCeEEEEEEEEcCceEEEEEE
Q 013709 236 KS----RPT-KSGKTIELDDVTFHQCVNLTRFNSEKTVSFVPPDGEFELMKYRITEGVNLPFRVLPTIKELGRTRMEVNV 310 (438)
Q Consensus 236 ~~----~~~-~~~~~~~l~d~~fH~cV~~~~f~~~~~i~F~PPdG~F~Lm~Yr~~~~~~~P~~v~~~~~~~~~~~~e~~l 310 (438)
+. .+. +....+.|+||+||+||++++|++++.|+|+||||+|+||+||++.+..+||+|.|.+++.|.+++|+++
T Consensus 239 ~~~n~~~~sks~~g~v~leDc~FHqCV~L~kFn~eh~IsFvPPDGe~ELMkYr~~enInlPFrV~PiV~el~r~kie~ri 318 (446)
T KOG0938|consen 239 DFGNKNFPSKSGKGSVLLEDCTFHQCVRLDKFNSEHIISFVPPDGEFELMKYRVTENINLPFRVTPIVTELGRTKIEYRI 318 (446)
T ss_pred cccccCCCcccCCceEEeeccchheeeccccccccceEEEeCCCCceEeEeeeeccCcccceEeeeheecccceeEEEEE
Confidence 11 122 2334599999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeecCCCceeeeeEEEEeeCCCCCceeEEEEceeEEEEeccCcEEEEEeeecCCCCeeEEEEEEEeeccccccCCCCCC
Q 013709 311 KIKSVFGAKMFALGVVIKIPVPKQTAKTSFQVTSGRAKYNASIDCLVWKIRKFPGQTEPTMSAEVELISTMAEKKSWTRP 390 (438)
Q Consensus 311 ~l~~~~~~~~~~~~v~i~ip~P~~~~~~~~~~~~G~~~~~~~~~~i~W~I~k~~g~~~~~l~~~~~~~~~~~~~~~~~~~ 390 (438)
.+++.|++++.+.+|.++||+|+++..+.++++.|+|+|.+.+++++|+|++++|.+|.+|++++++.+..++.+.|..|
T Consensus 319 ~iks~f~~kl~a~~v~~rIPvP~ntv~~n~~v~~Gkaky~psen~ivWki~kf~G~tE~tlsAevels~Tt~nkq~WtrP 398 (446)
T KOG0938|consen 319 TIKSLFPPKLLAKDVVVRIPVPPNTVKCNISVSNGKAKYVPSENAIVWKINKFNGLTESTLSAEVELSDTTQNKQQWTRP 398 (446)
T ss_pred EEeccCCchhhhcceEEEecCCCccccceeEEecCccccCcccceEEEEecccCCcccceeEEEEEeccCccccccccCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999998874467789999
Q ss_pred CeEEEEEeCcccccccEEEEEEEeec-CCCcccccEEEEEecCcEEEe
Q 013709 391 PIQMEFQVPMFTASGLRVRFLKVWEK-SGYNTVEWVRYITKAGSYEIR 437 (438)
Q Consensus 391 pi~v~F~i~~~t~SGl~V~~l~v~~~-~~~~~~k~vrY~t~sg~Y~~R 437 (438)
||+|+|++|||+.|||.|+|++|.++ ++|+..|||||+|+||+||+|
T Consensus 399 PIsleFeV~MFt~SGL~VrylkV~e~~Sk~~~vkWVrYitkaGsyEiR 446 (446)
T KOG0938|consen 399 PISLEFEVPMFTNSGLVVRYLKVSEKDSKHRAVKWVRYITKAGSYEIR 446 (446)
T ss_pred CceeEEeeeeecCCceEEEEEEEecccCCCceEEEEEEecccceeeeC
Confidence 99999999999999999999999984 599999999999999999998
No 2
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=4.2e-90 Score=671.36 Aligned_cols=421 Identities=44% Similarity=0.784 Sum_probs=379.8
Q ss_pred eEEEEEEeCCCCEEEEEcccCCCCCchHHHHHHhhccc-ccCCCCCeEEECCEEEEEEEeCcEEEEEEEcCCccHHHHHH
Q 013709 5 ASAIYFLNLRGDVLINRLYRDDVGGNMVDAFRTHIMQT-KELGTCPVRQIGGCSFFYMRISNVYIVIVVSSNANVACAFK 83 (438)
Q Consensus 5 I~~i~Il~~~G~~l~~r~y~~~~~~~~~~~f~~~v~~~-~~~~~~pi~~~~~~~~~~~~~~~l~~v~~~~~~~n~~~~~~ 83 (438)
++|+||+|.+|++|++|.||++.+.+..+.|.+++... .....+|++..+|.+|+|.+++++|++++++.|.+++.+++
T Consensus 1 ~sa~fild~~G~~lisr~yr~dv~~s~~~~F~~~l~~~e~~~~~~p~l~~~g~~~~~ik~s~lylv~~~~~n~~a~~v~~ 80 (424)
T KOG0937|consen 1 ASAVFILDHKGEVLISRDYRGDVPMSSTEKFFRKLFEKEEGDESPPFLVHDGSRFIHIKHSNLYLVAGTRPNVSAALVLS 80 (424)
T ss_pred CceEEEEcCCCcEeEeecccccCChhhhhhHHHHHhhhcccCCCCCeEEeCCceEEEEeecceEEEEEeccCCCHHHHHH
Confidence 58999999999999999999999999999999765542 22467899999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhcCCcCCHHHHHhhHHHHHHHHHHHHcCCeecccCHHHHhhhhhccCccCCCCCCCCCCCCCCCccccc
Q 013709 84 FVVEAVALFKSYFGGAFDEDAIRNNFVLIYELLDEIMDFGYPQNLSPEILKLYITQEGVRSPFSSKPTDRPVPNATLQVT 163 (438)
Q Consensus 84 ~L~~~~~vl~~y~~~~l~e~~i~~n~~~i~~lldE~id~G~p~~t~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ 163 (438)
||+++++++.+||+. +.|+.+++||+++||+|||++||||||.|+...|++++.+++++ ++....+.+.+.+
T Consensus 81 ~l~~~~~v~~~y~~~-l~e~si~~n~vlvyElLde~mDFGypQ~t~s~iL~~yi~~~~~~-------l~~~~~~~p~avt 152 (424)
T KOG0937|consen 81 FLYAVADVFGDYLSE-LEEESIRDNFVLVYELLDEVMDFGYPQTTDSEILKNYITQKANR-------LQDAQPRPPLAVT 152 (424)
T ss_pred HHHHHHHHHHHHhcc-CCccceecchHHHHHHHHHHhccCCcccchHHHHHHHhcccccc-------eeecCCCCCcccc
Confidence 999999999999997 99999999999999999999999999999999999999998762 2211112356778
Q ss_pred ceeecccCCCccccceEEEEEEEeEEEEEecccceEEEEEEEEEEEEEeecCCCeeEEEecCcccccccccccCCCCCCC
Q 013709 164 GAVGWRREGLVYKKNEVFLDIVESVNLLMSSKGSVLRCDVTGKILMKCFLSGMPDLKLGLNDKIGLEKESQLKSRPTKSG 243 (438)
Q Consensus 164 ~~~~WR~~~~~~~~nei~vdV~E~l~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~~ 243 (438)
++++||+.|++|+|||+|+||+|+|++.++++|.+++++|.|+|.|||+|+|||+++|+||+...++.. +..+.+
T Consensus 153 navsWrs~gi~~~KnevflDViE~Vs~l~~~~G~vl~s~i~G~I~~k~~LsGmPelrl~ln~~~~~~~~-----~~~~~s 227 (424)
T KOG0937|consen 153 NAVSWRSEGIYYGKNEVFLDVIESVSLLYDSNGIVLLSEIVGTIKLKCYLSGMPELRLGLNDKVLFDKQ-----GPRSKS 227 (424)
T ss_pred cceeecccccccccceEEEEhhhhhhHhhhcCCcEEEeeeeeEEEEEEEcCCCceeeeecCcccccccc-----cccccC
Confidence 899999999999999999999999999999999999999999999999999999999999998766553 223344
Q ss_pred ceEeeccceeeeeccccCccCcceEEEeCCCCeEEEEEEEecCCCCCCeEEEEEEEEcCceEEEEEEEEeecCCCceeee
Q 013709 244 KTIELDDVTFHQCVNLTRFNSEKTVSFVPPDGEFELMKYRITEGVNLPFRVLPTIKELGRTRMEVNVKIKSVFGAKMFAL 323 (438)
Q Consensus 244 ~~~~l~d~~fH~cV~~~~f~~~~~i~F~PPdG~F~Lm~Yr~~~~~~~P~~v~~~~~~~~~~~~e~~l~l~~~~~~~~~~~ 323 (438)
.++.++|++||+||++++|+.+|+|+|+||||+|+||+||.+...+|++.+.......+..++++.++++++|+.+..+.
T Consensus 228 ~~v~ledi~fh~~v~l~~fd~dr~i~FiPPdGeF~Lm~Y~ls~~vkPli~~~~~~~~~~~~ri~i~~K~~~~fk~~~~a~ 307 (424)
T KOG0937|consen 228 KGVELEDIKFHECVRLSRFDNDRTISFIPPDGEFELMRYRLSTHVKPLIWFYQLIEEHSRSRIEVMVKLREQFKSRSSAN 307 (424)
T ss_pred cceEeeecccceeechhhccCCceEEecCCCCceEEEEEEecCCCCCeEEeeeeeeeccceeEEEEEechhhcCCccccc
Confidence 67999999999999999999999999999999999999999988775555555555667889999999999999999999
Q ss_pred eEEEEeeCCCCCceeEEEEceeEEEEeccCcEEEEEeeecCCCCeeEEEEEEEeeccccccC-CCCCCCeEEEEEeCccc
Q 013709 324 GVVIKIPVPKQTAKTSFQVTSGRAKYNASIDCLVWKIRKFPGQTEPTMSAEVELISTMAEKK-SWTRPPIQMEFQVPMFT 402 (438)
Q Consensus 324 ~v~i~ip~P~~~~~~~~~~~~G~~~~~~~~~~i~W~I~k~~g~~~~~l~~~~~~~~~~~~~~-~~~~~pi~v~F~i~~~t 402 (438)
+|+|+||+|..++.+....+.|+++|.+++++++|+|++++|+.|.++++++.+++....+. ....+||+|+|+||++|
T Consensus 308 ~v~I~iP~P~~a~~~~fk~s~G~~~~~~e~~~l~W~I~~~~gg~e~~~r~~~~lp~~~~e~~~~~~~~pi~v~FeIp~~T 387 (424)
T KOG0937|consen 308 NVEICIPVPDDASSPSFKTSLGSAKYDPEKSALRWTIKKFVGGKEYSLRARMDLPSEEHEEQCTEGLGPIKVKFEIPYFT 387 (424)
T ss_pred eEEEEeeCCCccccceEeccCCceeeecccceEEEEeccccCCceEEEEEeecCCccccCCCCcccCCceEEEEEecccc
Confidence 99999999999999999999999999999999999999999999999999999987622221 34589999999999999
Q ss_pred ccccEEEEEEEeec-CCCcccccEEEEEecCcEEEeC
Q 013709 403 ASGLRVRFLKVWEK-SGYNTVEWVRYITKAGSYEIRC 438 (438)
Q Consensus 403 ~SGl~V~~l~v~~~-~~~~~~k~vrY~t~sg~Y~~R~ 438 (438)
.||++|+++++.++ .+|++.+||||.|+||.|++|+
T Consensus 388 ~SgiqVrylki~ep~~~y~s~~WVRy~T~s~~Y~~r~ 424 (424)
T KOG0937|consen 388 VSGIQVRYLKIIEPKSQYQSLPWVRYNTQSGPYEIRV 424 (424)
T ss_pred cCCeEEEEEEecccccCCCccceEEEEccCCceEeeC
Confidence 99999999999994 4999999999999999999995
No 3
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2e-79 Score=576.30 Aligned_cols=409 Identities=28% Similarity=0.495 Sum_probs=356.3
Q ss_pred eeEEEEEEeCCCCEEEEEcccC-CCCCchHHHHHHhhcccccC-CCCCeEEECCEEEEEEEeCcEEEEEEEcCCccHHHH
Q 013709 4 AASAIYFLNLRGDVLINRLYRD-DVGGNMVDAFRTHIMQTKEL-GTCPVRQIGGCSFFYMRISNVYIVIVVSSNANVACA 81 (438)
Q Consensus 4 mI~~i~Il~~~G~~l~~r~y~~-~~~~~~~~~f~~~v~~~~~~-~~~pi~~~~~~~~~~~~~~~l~~v~~~~~~~n~~~~ 81 (438)
||.+||++|.+|++++++++++ ...|++|+.|+..-....+. +.+|++....+.++.+.++++||++++..+..|+++
T Consensus 1 mi~siflidtsg~l~lek~~~g~t~~rsic~~f~e~~~~~~~~e~~ppvi~~p~hylfsv~~~~i~~~~~st~e~pPL~~ 80 (418)
T KOG2740|consen 1 MILSIFLIDTSGDLLLEKHLKGSTVVRSICDYFFEDQSSDDDLEHVPPVISTPHHYLFSVYRDLIFFCAVSTVETPPLMV 80 (418)
T ss_pred CeeEEEEEcCCchhhhhHhhCCceeeeehHHHHHHhhhhccccccCCceecCCceeeeeeeccCcEEEEEEeccCCChhH
Confidence 8999999999999999999995 45588999998876654332 455666777777777889999999999999999999
Q ss_pred HHHHHHHHHHHHhhcCCcCCHHHHHhhHHHHHHHHHHHHcCCeecccCHHHHhhhhhccCccC-CCCCC--CCCCCCCCC
Q 013709 82 FKFVVEAVALFKSYFGGAFDEDAIRNNFVLIYELLDEIMDFGYPQNLSPEILKLYITQEGVRS-PFSSK--PTDRPVPNA 158 (438)
Q Consensus 82 ~~~L~~~~~vl~~y~~~~l~e~~i~~n~~~i~~lldE~id~G~p~~t~~~~l~~~i~~~~~~~-~~~~~--~~~~~~~~~ 158 (438)
++||+++++++.+|||+ ++|.+|++|++.|||+||||+|+|+|..||+|+|+++|+.++..+ ++.+- +.+.+ .++
T Consensus 81 iefL~rv~dv~~eyFg~-~s~~~Ik~N~~vv~ell~emiDnGfpl~tE~NiLke~i~pps~l~~~~~svTg~~n~~-~~l 158 (418)
T KOG2740|consen 81 IEFLHRVVDVLLEYFGG-LSESKIKDNVVVVYELLDEMIDNGFPLVTEPNILKELIPPPSFLSKKFNSVTGNSNVS-DTL 158 (418)
T ss_pred HHHHHHHHHHHHHHhcc-cCHhHhhcceeeHHHHHHHHHHcCCCcccChhHHHhhcCChHHHHHHHhhhhcccccc-ccC
Confidence 99999999999999998 999999999999999999999999999999999999999887755 22110 11111 456
Q ss_pred cccccceeecccCCCccccceEEEEEEEeEEEEEecccceEEEEEEEEEEEEEeecCCCeeEEEecCcccccccccccCC
Q 013709 159 TLQVTGAVGWRREGLVYKKNEVFLDIVESVNLLMSSKGSVLRCDVTGKILMKCFLSGMPDLKLGLNDKIGLEKESQLKSR 238 (438)
Q Consensus 159 ~~~~~~~~~WR~~~~~~~~nei~vdV~E~l~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~ 238 (438)
|..+-+.+|||+++.+|.+||+||||+|+++|+++++|..+.++|.|.|.|+|+|+|||++.|.|+++
T Consensus 159 Ptg~~s~VPWR~~~~Ky~nNE~yvdvlEeidai~~k~gslv~~eI~g~vd~~~qLsgmPdltlsl~np------------ 226 (418)
T KOG2740|consen 159 PTGALSNVPWRTAGVKYTNNEAYVDVLEEIDAIVDKKGSLVFGEIQGIVDVCSQLSGMPDLTLSLNNP------------ 226 (418)
T ss_pred CCcccccccccccCcccccchhhhhhhheeheEecCCCCEEEEEEEEEEEEEEeecCCCceEEEccCc------------
Confidence 67778899999999999999999999999999999999999999999999999999999999999875
Q ss_pred CCCCCceEeeccceeeeeccccCccCcceEEEeCCCCeEEEEEEEecCC--CCCCeEEEEEEEEcCc--eEEEEEEEEee
Q 013709 239 PTKSGKTIELDDVTFHQCVNLTRFNSEKTVSFVPPDGEFELMKYRITEG--VNLPFRVLPTIKELGR--TRMEVNVKIKS 314 (438)
Q Consensus 239 ~~~~~~~~~l~d~~fH~cV~~~~f~~~~~i~F~PPdG~F~Lm~Yr~~~~--~~~P~~v~~~~~~~~~--~~~e~~l~l~~ 314 (438)
..|+|++|||||++.+|++++.|+|+||||+|+||+||++.. ..+|..+.++.+..+. +++++.+..+.
T Consensus 227 -------~~L~dvsfHpcVr~krwe~~~~lsFIPPDGkFrLlsy~v~~~~~v~~pvyv~~~i~l~~~~~~ri~~tvg~~~ 299 (418)
T KOG2740|consen 227 -------RLLGDVSFHPCVRYKRWESHSVLSFIPPDGKFRLLSYRVDAQNQVAIPVYVKNSISLDSNHQGRISLTVGPKK 299 (418)
T ss_pred -------cccCCcccccceeecccccccceEEcCCCCcEEEEEEEEehhhccccceEEeeeeccCCCceEEEEEeccccc
Confidence 468999999999999999999999999999999999999754 6789999999886543 33443333333
Q ss_pred cCCCceeeeeEEEEeeCCCCCceeEEEEceeEEEEeccCcEEEEEeeecCCCCeeEEEEEEEeeccccccCCCCCCCeEE
Q 013709 315 VFGAKMFALGVVIKIPVPKQTAKTSFQVTSGRAKYNASIDCLVWKIRKFPGQTEPTMSAEVELISTMAEKKSWTRPPIQM 394 (438)
Q Consensus 315 ~~~~~~~~~~v~i~ip~P~~~~~~~~~~~~G~~~~~~~~~~i~W~I~k~~g~~~~~l~~~~~~~~~~~~~~~~~~~pi~v 394 (438)
..+ ...+.+.|+...|+.+...+...++|+..++...+.+.|.++++..+.-+.|+|++++.++ .....+++.+++
T Consensus 300 ~~g--K~ie~itVt~~~pn~i~~~~k~~~~g~~~~~~~~k~l~W~~~~i~tg~lp~Lkg~~~~e~~--~sk~~~l~t~~L 375 (418)
T KOG2740|consen 300 KMG--KTIELITVTVQDPNEIAYASKILTHGTFTNSIIMKQLTWTFGSIATGKLPVLKGTINLEPG--FSKKVDLPTLSL 375 (418)
T ss_pred ccc--ceeEeEEEEecCccceeeeecccccceeEeecccceeEEEeecccCCcccccccccccCCC--CCccccCcccce
Confidence 333 3467789999999999888888899999999999999999999998888999999999875 344566899999
Q ss_pred EEEeCcccccccEEEEEEEeecCCCcccccEEEEEecCcEEEeC
Q 013709 395 EFQVPMFTASGLRVRFLKVWEKSGYNTVEWVRYITKAGSYEIRC 438 (438)
Q Consensus 395 ~F~i~~~t~SGl~V~~l~v~~~~~~~~~k~vrY~t~sg~Y~~R~ 438 (438)
+|++.+.++||++|+.|++.+ ..|+|||||||.|+||++++|+
T Consensus 376 qykiqg~alsglkVe~Ldm~~-~~~k~yKGvKy~t~agnfqvR~ 418 (418)
T KOG2740|consen 376 QYKIQGQALSGLKVERLDMYG-EPYKPYKGVKYKTKAGNFQVRL 418 (418)
T ss_pred eeeeeeeeccceEEEeeeecC-CCCccccceEEEEeeeeEEEeC
Confidence 999999999999999999987 4789999999999999999996
No 4
>PF00928 Adap_comp_sub: Adaptor complexes medium subunit family; InterPro: IPR008968 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. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) 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 [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. This entry represents the C-terminal domain of the mu subunit from various clathrin adaptors (AP1, AP2 and AP3) []. The C-teminal domain has an immunoglobulin-like beta-sandwich fold consisting of 9 strands in 2 sheets with a Greek key topology, similar to that found in cytochrome f and certain transcription factors []. The mu subunit regulates the coupling of clathrin lattices with particular membrane proteins by self-phosphorylation via a mechanism that is still unclear []. The mu subunit possesses a highly conserved N-terminal domain of around 230 amino acids, which may be the region of interaction with other AP proteins; a linker region of between 10 and 42 amino acids; and a less well-conserved C-terminal domain of around 190 amino acids, which may be the site of specific interaction with the protein being transported in the vesicle []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 1H6E_A 3L81_A 1W63_V 4EMZ_A 4EN2_A 2VGL_M 3ML6_F 2PR9_A 2JKT_M 1I31_A ....
Probab=100.00 E-value=1.1e-61 Score=466.98 Aligned_cols=261 Identities=43% Similarity=0.835 Sum_probs=220.1
Q ss_pred eecccCCCccccceEEEEEEEeEEEEEecccceEEEEEEEEEEEEEeecCCCeeEEEecCcccccccccccCCCCCCCce
Q 013709 166 VGWRREGLVYKKNEVFLDIVESVNLLMSSKGSVLRCDVTGKILMKCFLSGMPDLKLGLNDKIGLEKESQLKSRPTKSGKT 245 (438)
Q Consensus 166 ~~WR~~~~~~~~nei~vdV~E~l~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~~~~ 245 (438)
+|||+.+++|++|||||||.|+++++++++|.++.++|.|+|.|+|+|+|+|+|+|+||++... ..++
T Consensus 1 ~~wR~~~~~~~~nei~vdv~E~i~~~~~~~G~~~~~~v~G~v~~~~~l~g~p~i~l~l~~~~~~------------~~~~ 68 (262)
T PF00928_consen 1 VPWRPSGIKYKKNEIFVDVVEKISAVLDRDGNILSSEVKGSVQCKSFLSGMPEIKLTLNNPLVV------------SKNG 68 (262)
T ss_dssp -TTS-STB--SSEEEEEEEEEEEEEEEETTSEEEEEEEEEEEEEEEE-SST-EEEEEESSSCCC------------TSSS
T ss_pred CCcccCCcccccceEEEEEEEEEEEEEccCCcEEEEEEEEEEEEEEeCCCCCeEEEEecCcccc------------ccCc
Confidence 5899999999999999999999999999999999999999999999999999999999987533 2345
Q ss_pred EeeccceeeeeccccCccCcceEEEeCCCCeEEEEEEEecCCCCCCeEEEEEEEEcCceEEEEEEEEeecCCCceeeeeE
Q 013709 246 IELDDVTFHQCVNLTRFNSEKTVSFVPPDGEFELMKYRITEGVNLPFRVLPTIKELGRTRMEVNVKIKSVFGAKMFALGV 325 (438)
Q Consensus 246 ~~l~d~~fH~cV~~~~f~~~~~i~F~PPdG~F~Lm~Yr~~~~~~~P~~v~~~~~~~~~~~~e~~l~l~~~~~~~~~~~~v 325 (438)
+.++|++||||||+++|+++|.|+|+||||+|+||+||++....+||.+.|++...+++++++.+++++.++....+++|
T Consensus 69 ~~l~~~~fH~cV~~~~~~~~~~i~f~PPdg~f~Ll~Yr~~~~~~~P~~i~~~~~~~~~~~~~v~i~~~~~~~~~~~~~~v 148 (262)
T PF00928_consen 69 IKLDDVSFHPCVDLSKFESDRVISFIPPDGEFTLLRYRVSSNSPLPFKITCWVSEKSSGRFEVTIELESNFPNKISLENV 148 (262)
T ss_dssp BEESEEEEETTEECCCCCSHTEEEE---SEEEEEEEEEEESSS--SEEEEEEEEEETTTEEEEEEEEEE-S-TTSEEEEE
T ss_pred eeeeceeeccccCccccccccceecCCCCceEEEEEEEccCCCCCCcEEEEEeccCCCceEEEEEEecccCCCCceeceE
Confidence 78999999999999999999999999999999999999998889999999999887778999999999998888899999
Q ss_pred EEEeeCCCCCceeEEEEceeEEEEeccCcEEEEEeeecCCCCeeEEEEEEEeeccccccCCCCCCCeEEEEEeCcccccc
Q 013709 326 VIKIPVPKQTAKTSFQVTSGRAKYNASIDCLVWKIRKFPGQTEPTMSAEVELISTMAEKKSWTRPPIQMEFQVPMFTASG 405 (438)
Q Consensus 326 ~i~ip~P~~~~~~~~~~~~G~~~~~~~~~~i~W~I~k~~g~~~~~l~~~~~~~~~~~~~~~~~~~pi~v~F~i~~~t~SG 405 (438)
.|+||+|+++..+++..+.|+++|+.+++.++|+|++++++.+++|+|++++.........+.++||+|+|++|++++||
T Consensus 149 ~I~iplP~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~pi~v~F~~~~~~~Sg 228 (262)
T PF00928_consen 149 VIRIPLPPGTSSPSIESSDGSAEYDEEENALVWKIKKLPGGSESTLSGTLEFSSPSSVPSDWSFFPISVEFTIPGYTLSG 228 (262)
T ss_dssp EEEEE--TTEEEEEEEESSSEEEEETGCTEEEEEEEEEETSEEEEEEEEEEEEEECCSS-S-----EEEEEEESTSETTT
T ss_pred EEEeecCCccccceeeecCceEEEEccCCEEEEEECCccCcccccEEEEEEecCCCcccccccceeEEEEEEeCCcccCC
Confidence 99999999999999999999999999999999999999999999999999997653222334689999999999999999
Q ss_pred cEEEEEEEeec-CCCcccccEEEEEecCcEEEeC
Q 013709 406 LRVRFLKVWEK-SGYNTVEWVRYITKAGSYEIRC 438 (438)
Q Consensus 406 l~V~~l~v~~~-~~~~~~k~vrY~t~sg~Y~~R~ 438 (438)
++|++++|.+. .+|+|+|||||+|+||+|++|+
T Consensus 229 l~V~~l~v~~~~~~~~~~k~vky~t~s~~Y~iR~ 262 (262)
T PF00928_consen 229 LKVRSLDVVNEDENYKPYKWVKYVTKSGSYEIRT 262 (262)
T ss_dssp -EEEEEEEE-SSCGGGSEEEEEEEEEEEEEEE--
T ss_pred CEEEEEEeEecCCCCCCcccEEEEEEcCcEEEcC
Confidence 99999999884 4899999999999999999996
No 5
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.7e-42 Score=333.83 Aligned_cols=398 Identities=18% Similarity=0.283 Sum_probs=308.9
Q ss_pred ceeEEEEEEeCCCCEEEEEcccCCCC---CchHHHHHHhhcccccCCCCCeEEECCEEEEEEEeCcEEEEEEEcCCccHH
Q 013709 3 VAASAIYFLNLRGDVLINRLYRDDVG---GNMVDAFRTHIMQTKELGTCPVRQIGGCSFFYMRISNVYIVIVVSSNANVA 79 (438)
Q Consensus 3 ~mI~~i~Il~~~G~~l~~r~y~~~~~---~~~~~~f~~~v~~~~~~~~~pi~~~~~~~~~~~~~~~l~~v~~~~~~~n~~ 79 (438)
||+-++.|+++.|+.+++|+|+++.. ..++..|.+.+.. +.++.+++.++++|+|++.+++|+|.+|+.+.|++
T Consensus 1 Mvvlaa~i~t~~Gk~ivsRqf~~Msr~RIEgLl~aFpkLv~~---~~qhT~vEt~~VRYVYqP~d~lY~vLITtk~SNIl 77 (512)
T KOG2635|consen 1 MVVLAASINTKTGKAIVSRQFREMSRSRIEGLLAAFPKLVSA---GKQHTFVETDSVRYVYQPLDNLYIVLITTKQSNIL 77 (512)
T ss_pred CeEEEEEEeecCCceeeehHhHhhhHHHHHHHHHHhHHhhcc---CCCccEEecccEEEEEEecccEEEEEEeccccchh
Confidence 89999999999999999999994433 2477889887652 47999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhcCCcCCHHHHHhhHHHHHHHHHHHHcCCeecccCHHHHhhhhhccCccCCCCC-----------
Q 013709 80 CAFKFVVEAVALFKSYFGGAFDEDAIRNNFVLIYELLDEIMDFGYPQNLSPEILKLYITQEGVRSPFSS----------- 148 (438)
Q Consensus 80 ~~~~~L~~~~~vl~~y~~~~l~e~~i~~n~~~i~~lldE~id~G~p~~t~~~~l~~~i~~~~~~~~~~~----------- 148 (438)
..+++|+.|.+++.+||.. ++|+.|.+|.+.+...|||++..||....+..+++.|..|++|++++-.
T Consensus 78 eDl~TL~Lfskvipey~~s-lde~eI~~~~FelifAFDEivsLGyre~v~laQikty~eMdSHEEKi~e~v~~nke~ea~ 156 (512)
T KOG2635|consen 78 EDLETLRLFSKVIPEYCSS-LDEKEILENAFELIFAFDEIVSLGYRENVNLAQIKTYLEMDSHEEKIHELVMRNKEREAK 156 (512)
T ss_pred hHHHHHHHHHHhchhhhhh-hhHHHHHHhhhhhhhccchhhhhcccccccHHHhhhhhccccHHHHHHHHHHHhhhHHHH
Confidence 9999999999999999999 9999999999999999999999999999999999999999999753210
Q ss_pred -------CCCCC--------C-----------------C------------CCCc---c-cccceee-------------
Q 013709 149 -------KPTDR--------P-----------------V------------PNAT---L-QVTGAVG------------- 167 (438)
Q Consensus 149 -------~~~~~--------~-----------------~------------~~~~---~-~~~~~~~------------- 167 (438)
+++|+ . . ...+ + ++.++.|
T Consensus 157 q~mkrKaKElqr~r~ea~rrgg~~~~~~~~~~s~g~~~~s~~~~~~~~~~~~~~~~~~sa~~~~s~pak~mklG~k~~~s 236 (512)
T KOG2635|consen 157 QEMKRKAKELQRARKEAERRGGSLNPGFDAIGSSGYSSVSTTNAINRVESIAQKPKQQSAAKASSAPAKAMKLGKKTKNS 236 (512)
T ss_pred HHHHHHHHHHHHHHHhhhccccccCCCccccccccccCCcccchhhccccccccccccccccCCCCCchhhhhcccccch
Confidence 00000 0 0 0000 0 0000000
Q ss_pred ----------------------c------ccCCCccccceEEEEEEEeEEEEEecccceEEEEEEEEEEEEEeecCCCee
Q 013709 168 ----------------------W------RREGLVYKKNEVFLDIVESVNLLMSSKGSVLRCDVTGKILMKCFLSGMPDL 219 (438)
Q Consensus 168 ----------------------W------R~~~~~~~~nei~vdV~E~l~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~ 219 (438)
- .+......+|.+++.+.|+|++.+++||++.++++.|.+.++..-.--..+
T Consensus 237 ~~~~d~Lk~ege~ia~~~s~~g~~s~aap~~~~p~v~~e~v~i~ieEkln~~~~RDGgi~s~E~qG~lsLrI~d~e~~~i 316 (512)
T KOG2635|consen 237 DTFVDKLKGEGERIAGASSAIGSASSAAPPPTAPDVPEESVHIVIEEKLNVRLSRDGGIKSGEVQGTLSLRIKDEEYGDI 316 (512)
T ss_pred hhHHHHhhccccccccccccccccccCCCCCCCCCCccceEEEEEeeeEeEEEcccCCccceeeeeeEEEEEccccccce
Confidence 0 001112245669999999999999999999999999999999988888889
Q ss_pred EEEecCcccccccccccCCCCCCCceEeeccceeeeeccccCccCcceEEEeCCCCeEE------EEEEEecC--CCCCC
Q 013709 220 KLGLNDKIGLEKESQLKSRPTKSGKTIELDDVTFHQCVNLTRFNSEKTVSFVPPDGEFE------LMKYRITE--GVNLP 291 (438)
Q Consensus 220 ~l~ln~~~~~~~~~~~~~~~~~~~~~~~l~d~~fH~cV~~~~f~~~~~i~F~PPdG~F~------Lm~Yr~~~--~~~~P 291 (438)
.|.|++.. ..+ -++++||++|++.|.++..|.+.+|+..|+ |++||... ...+|
T Consensus 317 ~lkl~n~~---------------~~g---~q~ktHPNlDK~~f~s~s~iglk~~~K~FPvn~~VGvLkWR~~~~des~iP 378 (512)
T KOG2635|consen 317 ELKLANGR---------------DKG---TQLKTHPNLDKKVFLSSSLIGLKRPEKPFPVNSDVGVLKWRMVDEDESEIP 378 (512)
T ss_pred EEEEcCCC---------------Ccc---eeeeeCCCcchhhhccccccccccCCCCCCcCCcceEEEEeecccccccCc
Confidence 99997631 122 357999999999999999999999999995 89999965 46789
Q ss_pred eEEEEEEEEcCce-EEEEEEEEeecCCCceeeeeEEEEeeCCCCCceeEEEEceeEEEEeccCcEEEEEeeecCCCCeeE
Q 013709 292 FRVLPTIKELGRT-RMEVNVKIKSVFGAKMFALGVVIKIPVPKQTAKTSFQVTSGRAKYNASIDCLVWKIRKFPGQTEPT 370 (438)
Q Consensus 292 ~~v~~~~~~~~~~-~~e~~l~l~~~~~~~~~~~~v~i~ip~P~~~~~~~~~~~~G~~~~~~~~~~i~W~I~k~~g~~~~~ 370 (438)
++++||.++.|.+ .+.++..+.. ...+.||.|.||+|.++ .+++...+|.+.|+..++.+.|+|+.+..+...+
T Consensus 379 lTincWPSes~~g~dV~iEYe~~~----~~eL~dV~i~iPlP~~i-apsv~~~Dge~~~~~~~~~leW~I~~Ia~N~SGs 453 (512)
T KOG2635|consen 379 LTINCWPSESGNGYDVNIEYEAVL----ECELNDVIITIPLPANI-APSVGECDGEYRYDERKNVLEWSIGVIAKNFSGS 453 (512)
T ss_pred eEEEeccccCCCCeEEEEEEeehh----cccccceEEEeeccccc-CCccceecceEEeccccceeEEEeeeeccCCCCc
Confidence 9999999986543 3322222221 23578999999999998 7888899999999999999999999995444333
Q ss_pred EEEEEEeeccccccCCCCCCCeEEEEEeCcccccccEEEEEEEeecCCCccccc-EEEEEecCcEEE
Q 013709 371 MSAEVELISTMAEKKSWTRPPIQMEFQVPMFTASGLRVRFLKVWEKSGYNTVEW-VRYITKAGSYEI 436 (438)
Q Consensus 371 l~~~~~~~~~~~~~~~~~~~pi~v~F~i~~~t~SGl~V~~l~v~~~~~~~~~k~-vrY~t~sg~Y~~ 436 (438)
| +|.++. .++..++|++|.|... .+++|+.|..+.-.. .+ .|.++ ++-.-.+..|++
T Consensus 454 l--EFs~~~----~~~~~fFPl~VsF~s~-~~ftgl~vqkVv~~~-~~-~~~~y~~~t~f~~dky~V 511 (512)
T KOG2635|consen 454 L--EFSCPA----SDPDGFFPLSVSFTSD-TVFTGLFVQKVVRND-GH-APVRYSVETTFEVDKYEV 511 (512)
T ss_pred E--EEeecC----CCCCceeeEEEEEEec-ccccceEEEEEEEcC-CC-CCceeEEEEEEEeeeeEe
Confidence 3 233332 4566799999999988 799999999975543 22 23222 232233677875
No 6
>KOG2677 consensus Stoned B synaptic vesicle biogenesis protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.7e-37 Score=309.59 Aligned_cols=259 Identities=29% Similarity=0.505 Sum_probs=217.2
Q ss_pred CccccceEEEEEEEeEEEEEecccceEEEEEEEEEEEEEeecCCCeeEEEecCcccccccccc--cCCCCCCCceEeecc
Q 013709 173 LVYKKNEVFLDIVESVNLLMSSKGSVLRCDVTGKILMKCFLSGMPDLKLGLNDKIGLEKESQL--KSRPTKSGKTIELDD 250 (438)
Q Consensus 173 ~~~~~nei~vdV~E~l~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~~~--~~~~~~~~~~~~l~d 250 (438)
..|..+||.|||.++.++.++++|.++...|..+|.|.|||+|+|+|.|+|||..+.|++... +..+.....|+.|.+
T Consensus 582 ~nY~e~EI~v~~~Defsg~V~Keg~~~~~~v~tri~cL~FlsG~~ec~lgLND~~~kg~Eiv~rkDimp~~t~kwI~~~~ 661 (922)
T KOG2677|consen 582 SNYLEEEITVDVRDEFSGIVSKEGQILQHHVLTRIHCLSFLSGLAECRLGLNDILVKGNEIVLRKDIMPTTTTKWIKLHE 661 (922)
T ss_pred cccccceeEEEEEeccceeecccchhhhhhhhhhhhhhhhccCCceeEeecchhhhcccceeEeccccccccccceeeee
Confidence 468999999999999999999999999999999999999999999999999998887766543 445566778999999
Q ss_pred ceeeeeccccCccCcceEEEeCCCC-eEEEEEEEecCC-CCCCeEEEEEEEEcCceEEEEEEEE--ee------cCCCce
Q 013709 251 VTFHQCVNLTRFNSEKTVSFVPPDG-EFELMKYRITEG-VNLPFRVLPTIKELGRTRMEVNVKI--KS------VFGAKM 320 (438)
Q Consensus 251 ~~fH~cV~~~~f~~~~~i~F~PPdG-~F~Lm~Yr~~~~-~~~P~~v~~~~~~~~~~~~e~~l~l--~~------~~~~~~ 320 (438)
|.||-||+.+.|+++|+|.|.|||| +|+|||||+..+ ..+||.++..+...| ..||+..-+ .+ .-....
T Consensus 662 ~~FH~cVn~~eF~~srVI~F~PlDaCrFElMRFrt~~~~~~lpftlks~~~V~G-a~VEvq~~~~mat~~qr~rd~~~~v 740 (922)
T KOG2677|consen 662 CRFHGCVNEDEFHNSRVILFNPLDACRFELMRFRTVFAEKTLPFTLKSATSVNG-AEVEVQSWLRMATGFQRNRDPLTQV 740 (922)
T ss_pred eeeecccchhhccccceEEecCcccceeeeeeeeeecCCCcCceeeeeeeeecc-ceeehHHHHHHHhhhhhccCccccC
Confidence 9999999999999999999999999 599999999754 589999998887765 467765322 22 223567
Q ss_pred eeeeEEEEeeCCCCC--------------------------------ceeEEEEceeEEEEeccCcEEEEEeeecCCC--
Q 013709 321 FALGVVIKIPVPKQT--------------------------------AKTSFQVTSGRAKYNASIDCLVWKIRKFPGQ-- 366 (438)
Q Consensus 321 ~~~~v~i~ip~P~~~--------------------------------~~~~~~~~~G~~~~~~~~~~i~W~I~k~~g~-- 366 (438)
.|+||.|++|+|..+ ..+.++++.|+++|++..+.++|+|++++.+
T Consensus 741 pCenI~IrfPVPs~WIk~fr~e~~~g~kSlkaK~nR~a~~gsl~~~~sepvi~vt~G~AKYEhay~siVWrI~RLPdKns 820 (922)
T KOG2677|consen 741 PCENIMIRFPVPSEWIKNFRRESVLGEKSLKAKVNRGASFGSLSVSGSEPVIRVTLGTAKYEHAYNSIVWRINRLPDKNS 820 (922)
T ss_pred cccceeEeccCcHHHHHHHHHHhhhccchhhhhhcccccccchhhccCCceEEEeecchhhHHhhhhheeecccCCcccc
Confidence 899999999999743 1345789999999999999999999999865
Q ss_pred ---CeeEEEEEEEeeccccccCCCCCCCeEEEEEeCcccccccEEEEEEEeecCCCcccccEEEEEecCcEEE
Q 013709 367 ---TEPTMSAEVELISTMAEKKSWTRPPIQMEFQVPMFTASGLRVRFLKVWEKSGYNTVEWVRYITKAGSYEI 436 (438)
Q Consensus 367 ---~~~~l~~~~~~~~~~~~~~~~~~~pi~v~F~i~~~t~SGl~V~~l~v~~~~~~~~~k~vrY~t~sg~Y~~ 436 (438)
..+.|.|.++|.+.+..+..| .+.+.|+|.+|..++|...||+|.|.. .-.+.|||+|... -+|++
T Consensus 821 a~~hpHcl~c~lELgSd~evPs~f-~p~~~V~FsmP~t~aS~t~VRSisVE~--~~~v~K~V~y~A~-Y~yqv 889 (922)
T KOG2677|consen 821 ASGHPHCLFCHLELGSDREVPSRF-APHVNVEFSMPTTSASKTSVRSISVED--KTDVRKWVNYSAH-YSYQV 889 (922)
T ss_pred ccCCCeeEEEEEeccccccCchhh-ccccceeeeccccccccceeeeeeccc--cccHHHHHhhhhh-eeeee
Confidence 368899999998864333333 677999999999999999999999966 3469999999654 44554
No 7
>PF01217 Clat_adaptor_s: Clathrin adaptor complex small chain; InterPro: IPR022775 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 small sigma and mu subunits of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and the zeta and delta subunits of various coatomer (COP) adaptors. The small sigma subunit of AP proteins have been characterised in several species [, , , ]. The sigma subunit plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The zeta subunit of coatomers (zeta-COP) is required for coatomer binding to Golgi membranes and for coat-vesicle assembly [, ]. More information about these proteins can be found at Protein of the Month: Clathrin [].; PDB: 1W63_W 2JKR_I 2VGL_S 2JKT_I 2XA7_S 2HF6_A 3TJZ_C.
Probab=99.95 E-value=4.5e-27 Score=205.10 Aligned_cols=135 Identities=27% Similarity=0.473 Sum_probs=116.6
Q ss_pred eeEEEEEEeCCCCEEEEEcccCCCCCc---hHHHHHHhhcccccCCCCCeEEECCEEEEEEEeCcEEEEEEEcCCccHHH
Q 013709 4 AASAIYFLNLRGDVLINRLYRDDVGGN---MVDAFRTHIMQTKELGTCPVRQIGGCSFFYMRISNVYIVIVVSSNANVAC 80 (438)
Q Consensus 4 mI~~i~Il~~~G~~l~~r~y~~~~~~~---~~~~f~~~v~~~~~~~~~pi~~~~~~~~~~~~~~~l~~v~~~~~~~n~~~ 80 (438)
||+|++|+|++|+++++|+|++...+. ..+.+.+.+..++ ...+|++.+++++++|++.++|||+++++.++|+++
T Consensus 1 MI~~i~i~n~~G~~i~~k~y~~~~~~~~~~~~~~~~~~~~~~~-~~~~~i~~~~~~~~vy~~~~dl~~~~v~~~~eNel~ 79 (141)
T PF01217_consen 1 MIKAILILNSQGKRILSKYYRDVSEEERQKLFEKFIKKKSSRN-SKQSPIFEHDNYRIVYKRYSDLYFVVVGDENENELL 79 (141)
T ss_dssp SEEEEEEEETTSEEEEEEESSTSTSHHHHHHHHHHHHHHHTSS-SSSTSEEEETTEEEEEEEETTEEEEEEESSTSBHHH
T ss_pred CEEEEEEEcCCCCEEEehhcCCccHHHHHHHHHHHHHHHHhcc-cccceeeecccceeeeEeeccEEEEEEeecccchHH
Confidence 899999999999999999996554432 3344444444333 256999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhcCCcCCHHHHHhhHHHHHHHHHHHHcCCeecccCHHHHhhhhhcc
Q 013709 81 AFKFVVEAVALFKSYFGGAFDEDAIRNNFVLIYELLDEIMDFGYPQNLSPEILKLYITQE 140 (438)
Q Consensus 81 ~~~~L~~~~~vl~~y~~~~l~e~~i~~n~~~i~~lldE~id~G~p~~t~~~~l~~~i~~~ 140 (438)
++++|++++++|++||+. ++|..|++||+.+|++||||+|+|+|++||++.|..++.+.
T Consensus 80 ~~e~l~~~v~~l~~~~~~-v~e~~i~~N~~~v~~~LDEiid~G~i~etd~~~I~~~v~~~ 138 (141)
T PF01217_consen 80 LLEFLHRLVEVLDDYFGN-VSEKDILENFDLVYLILDEIIDGGIILETDPNVILKRVTMQ 138 (141)
T ss_dssp HHHHHHHHHHHHHHHHSS--SHHHHHHTHHHHHHHHHHHEETTEES--THHHHHHHHHHC
T ss_pred HHHHHHHhhhhhhhhhcc-ccHHHHHHCHHHHHHHHHHHHhCCEEEECCHHHHHHHHHHh
Confidence 999999999999999997 99999999999999999999999999999999999998864
No 8
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=99.83 E-value=6.1e-20 Score=151.59 Aligned_cols=133 Identities=17% Similarity=0.230 Sum_probs=119.6
Q ss_pred eeEEEEEEeCCCCEEEEEcccCCCC---CchHHHHHHhhcccccCCCCCeEEECCEEEEEEEeCcEEEEEEEcCCccHHH
Q 013709 4 AASAIYFLNLRGDVLINRLYRDDVG---GNMVDAFRTHIMQTKELGTCPVRQIGGCSFFYMRISNVYIVIVVSSNANVAC 80 (438)
Q Consensus 4 mI~~i~Il~~~G~~l~~r~y~~~~~---~~~~~~f~~~v~~~~~~~~~pi~~~~~~~~~~~~~~~l~~v~~~~~~~n~~~ 80 (438)
||++++|+|++|++++.|||.+... ..+++..++.+.+++. +++.+++..+.+.+|+++++|||+++.+.++|++.
T Consensus 1 ~i~~vli~nrqgk~RL~K~yt~~~~~e~~kli~~i~~lIs~R~~-ke~N~~e~k~~kiVYrrYA~LyF~f~Vd~~dnEl~ 79 (152)
T COG5030 1 MIKFVLIFNRQGKPRLVKWYTPVSDPEQAKLIADIYELISARKP-KESNFIEGKNEKIVYRRYATLYFVFGVDNDDNELI 79 (152)
T ss_pred CeEEEEEEcCCCceeeeEeeccCCcHHHHHHHHHHHHHHHcCCc-hhcccccccCcEEEeeecCcEEEEEEEcCCCCcch
Confidence 8999999999999999999976433 2366677778777654 68899999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhcCCcCCHHHHHhhHHHHHHHHHHHHcCCeecccCHHHHhhhhh
Q 013709 81 AFKFVVEAVALFKSYFGGAFDEDAIRNNFVLIYELLDEIMDFGYPQNLSPEILKLYIT 138 (438)
Q Consensus 81 ~~~~L~~~~~vl~~y~~~~l~e~~i~~n~~~i~~lldE~id~G~p~~t~~~~l~~~i~ 138 (438)
+|+++|.|+++|+.|||+ +||..+..||-.+|.+||||+-+|..++++++.+-+.+.
T Consensus 80 iL~lIh~FVE~lDr~Fgn-VCELdlIFNF~kv~~ILdE~i~gG~i~Es~~~~vl~~v~ 136 (152)
T COG5030 80 ILELIHNFVEILDRFFGN-VCELDLIFNFQKVYAILDEMILGGEIIESSKNEVLEHVY 136 (152)
T ss_pred HHHHHHHHHHHHHHHhcc-ceeeEeEeeHHHHHHHHHHHHhCCeeeecCHHHHHHHHH
Confidence 999999999999999999 999999999999999999999999999999987665443
No 9
>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.77 E-value=3.3e-18 Score=144.53 Aligned_cols=140 Identities=16% Similarity=0.257 Sum_probs=129.5
Q ss_pred eeEEEEEEeCCCCEEEEEcccCCCCC--chHHHHHHhhcccccCCCCCeEEECCEEEEEEEeCcEEEEEEEcCCccHHHH
Q 013709 4 AASAIYFLNLRGDVLINRLYRDDVGG--NMVDAFRTHIMQTKELGTCPVRQIGGCSFFYMRISNVYIVIVVSSNANVACA 81 (438)
Q Consensus 4 mI~~i~Il~~~G~~l~~r~y~~~~~~--~~~~~f~~~v~~~~~~~~~pi~~~~~~~~~~~~~~~l~~v~~~~~~~n~~~~ 81 (438)
.+++++|+|++|+++++|||.++.+. ....+|.+.+.+...+.+..|..++|...+|+..-||+|..+...++|+++.
T Consensus 8 ~vk~iliLD~~G~Ri~aKYY~~~~~s~vkeqkaFEK~lF~KT~kt~~eI~~ldg~~vvYk~~~Dl~fyv~G~~~ENEl~L 87 (175)
T KOG3343|consen 8 TVKAILILDSDGKRILAKYYDDPHPSTVKEQKAFEKNLFSKTSKTESEILLLDGNTVVYKSVIDLHFYVVGSEEENELML 87 (175)
T ss_pred hhheEEEEcCCCCEeeeeecCCCcchhHHHHHHHHHHHhcccccccceeEEecCcEEEEEecccEEEEEecCcchhHHHH
Confidence 57899999999999999999988775 3567899999876666788899999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhcCCcCCHHHHHhhHHHHHHHHHHHHcCCeecccCHHHHhhhhhccCcc
Q 013709 82 FKFVVEAVALFKSYFGGAFDEDAIRNNFVLIYELLDEIMDFGYPQNLSPEILKLYITQEGVR 143 (438)
Q Consensus 82 ~~~L~~~~~vl~~y~~~~l~e~~i~~n~~~i~~lldE~id~G~p~~t~~~~l~~~i~~~~~~ 143 (438)
.+.|+.|.+.+.-.+.+.+....+.+|++.+..++|||||+|.+++||++++..++...+..
T Consensus 88 ~svL~~l~dal~llLr~nveKr~llEN~D~i~L~~DEiiD~GvILEtdp~~ia~rv~~~~~~ 149 (175)
T KOG3343|consen 88 MSVLTCLFDALSLLLRKNVEKRELLENLDLIFLALDEIIDGGVILETDPNQIAQRVALRPTD 149 (175)
T ss_pred HHHHHHHHHHHHHHHHhChhHHHHHhhhccceeehhhhccCceEEecCHHHHHHHhccCCCC
Confidence 99999999999999998889999999999999999999999999999999999999987764
No 10
>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.74 E-value=1.2e-17 Score=134.23 Aligned_cols=134 Identities=16% Similarity=0.164 Sum_probs=112.1
Q ss_pred eeEEEEEEeCCCCEEEEEcccCCCC--C-chHHHHHHhhcccccCCCCCeEEECCEEEEEEEeCcEEEEEEEcCCccHHH
Q 013709 4 AASAIYFLNLRGDVLINRLYRDDVG--G-NMVDAFRTHIMQTKELGTCPVRQIGGCSFFYMRISNVYIVIVVSSNANVAC 80 (438)
Q Consensus 4 mI~~i~Il~~~G~~l~~r~y~~~~~--~-~~~~~f~~~v~~~~~~~~~pi~~~~~~~~~~~~~~~l~~v~~~~~~~n~~~ 80 (438)
||..|+|.|+.|+.+++|||.+-.. + .+.+...+.+..+..+.+..+.........++++++|||+...+...|.+.
T Consensus 1 mi~FILiqNr~Gk~RLak~yv~~dd~ek~~~~~~vh~lvs~Rd~K~~~~~~~~~~~~~~~rryagLyf~~~vd~tDnela 80 (143)
T KOG0935|consen 1 MIRFILIQNRAGKTRLAKWYVQFDDDEKQKLIEEVHALVTVRDAKHTNFVEFRNFKIIYRRRYAGLYFCICVDVTDNELA 80 (143)
T ss_pred CeEEEEEEccccceeheeeeeccCchHHHHHHHHHHHHHhhccchhhhheeeeeceEEEEEeeCCEEEEEEEecCCchHH
Confidence 8999999999999999999975433 2 355666666666554344445455555555579999999999999999999
Q ss_pred HHHHHHHHHHHHHhhcCCcCCHHHHHhhHHHHHHHHHHHHcCCeecccCHHHHhhhhh
Q 013709 81 AFKFVVEAVALFKSYFGGAFDEDAIRNNFVLIYELLDEIMDFGYPQNLSPEILKLYIT 138 (438)
Q Consensus 81 ~~~~L~~~~~vl~~y~~~~l~e~~i~~n~~~i~~lldE~id~G~p~~t~~~~l~~~i~ 138 (438)
.++.+|.|+++|++||++ ++|.++..||..||.++|||+-+|..++|+...+-+.+.
T Consensus 81 yLe~IHlFVEvLd~fF~N-VCELDlvFNFyKVy~i~DEm~l~GEi~Etsk~~vlerl~ 137 (143)
T KOG0935|consen 81 YLEHIHLFVEVLDEFFHN-VCELDLVFNFYKVYTIVDEMFLAGEIRETSKTKVLERLL 137 (143)
T ss_pred HHHHHHHHHHHHHHHhcc-ccceeeeeeeeeHHHHHHHHHHhhhhhhhhHHHHHHHHH
Confidence 999999999999999999 999999999999999999999999999999887766554
No 11
>KOG0934 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.73 E-value=2.7e-18 Score=141.78 Aligned_cols=127 Identities=20% Similarity=0.288 Sum_probs=112.3
Q ss_pred eeEEEEEEeCCCCEEEEEcccCCCC--Cc-hHHHHHHhhcccccCCCCCeEEECCEEEEEEEeCcEEEEEEEcCCccHHH
Q 013709 4 AASAIYFLNLRGDVLINRLYRDDVG--GN-MVDAFRTHIMQTKELGTCPVRQIGGCSFFYMRISNVYIVIVVSSNANVAC 80 (438)
Q Consensus 4 mI~~i~Il~~~G~~l~~r~y~~~~~--~~-~~~~f~~~v~~~~~~~~~pi~~~~~~~~~~~~~~~l~~v~~~~~~~n~~~ 80 (438)
||.++++.+++|+.+++|||..... |. ......+.+++++. ..+.+++..+...+|++++.|||++....+.|++.
T Consensus 1 mi~f~LlvsrQGk~rL~k~y~~~~~~er~~i~re~i~~~Lar~p-k~csfie~kd~kvVyrryasl~f~~~v~~~dNEL~ 79 (145)
T KOG0934|consen 1 MIKFFLLVSRQGKTRLQKWYEALSIKERKKIERELIKSVLARKP-KMCSFIEYKDEKVVYRRYASLFFCVGVEDNDNELA 79 (145)
T ss_pred CeEEEEEEeccCceehhHHHhhhcHHHHHHHHHHHHHHHHhCCc-ccccchhccCceehhhhhhhEEEEEEEecCCchhh
Confidence 7999999999999999999975433 22 33455556666554 68899999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhcCCcCCHHHHHhhHHHHHHHHHHHHcCCeecccCHHH
Q 013709 81 AFKFVVEAVALFKSYFGGAFDEDAIRNNFVLIYELLDEIMDFGYPQNLSPEI 132 (438)
Q Consensus 81 ~~~~L~~~~~vl~~y~~~~l~e~~i~~n~~~i~~lldE~id~G~p~~t~~~~ 132 (438)
+||++|+++++|+.|||+ ++|.+|..||..+|.+|||++-.|..+++..+.
T Consensus 80 ~LE~IH~~vE~lDkYFg~-VCELDiiFNfekay~ILde~~~~g~~~e~~k~~ 130 (145)
T KOG0934|consen 80 ILEFIHNYVELLDKYFGS-VCELDIIFNFEKAYFILDEFLLGGEIQETSKND 130 (145)
T ss_pred HHHHHHHHHHHHHHHhcc-ceeeEEEEehHhHHHHHHHHhcCcchHhhhccc
Confidence 999999999999999999 999999999999999999999999988887653
No 12
>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.71 E-value=5.5e-17 Score=135.81 Aligned_cols=134 Identities=14% Similarity=0.201 Sum_probs=116.2
Q ss_pred eeEEEEEEeCCCCEEEEEcccCCCC---CchHHHHHHhhcccccCCCCCeEEE------CCEEEEEEEeCcEEEEEEEcC
Q 013709 4 AASAIYFLNLRGDVLINRLYRDDVG---GNMVDAFRTHIMQTKELGTCPVRQI------GGCSFFYMRISNVYIVIVVSS 74 (438)
Q Consensus 4 mI~~i~Il~~~G~~l~~r~y~~~~~---~~~~~~f~~~v~~~~~~~~~pi~~~------~~~~~~~~~~~~l~~v~~~~~ 74 (438)
||+|++|+|.+|++++.|+|.+..- +.+++.-+..+.++++ ..+.+.+. .+.+.+|+++..|||+.+.+.
T Consensus 1 MI~AvlifNn~gkPRL~KFY~p~~~~~Qq~lir~vf~lvs~R~~-n~~nFLe~~~l~g~~d~rlIYrhYATLYFvfvvD~ 79 (182)
T KOG0936|consen 1 MIKAVLIFNNKGKPRLVKFYTPVDEEKQQQLIREVFHLVSKRPD-NVCNFLEGNSLIGGSDNRLIYRHYATLYFVFVVDS 79 (182)
T ss_pred CeeEEEEecCCCCcceeeecCcCChHHHHHHHHHHHHHHHcCCc-hHhhhhccccccCCccceeehheeeeEEEEEEEcC
Confidence 8999999999999999999986422 3456666667666664 44555443 358899999999999999999
Q ss_pred CccHHHHHHHHHHHHHHHHhhcCCcCCHHHHHhhHHHHHHHHHHHHcCCeecccCHHHHhhhhhc
Q 013709 75 NANVACAFKFVVEAVALFKSYFGGAFDEDAIRNNFVLIYELLDEIMDFGYPQNLSPEILKLYITQ 139 (438)
Q Consensus 75 ~~n~~~~~~~L~~~~~vl~~y~~~~l~e~~i~~n~~~i~~lldE~id~G~p~~t~~~~l~~~i~~ 139 (438)
.++++.+|++++.|++.|+..|.. ++|.++..|+..++.+|+|++.+|.+.+|+.|.+..-+..
T Consensus 80 sEsEL~iLDLIQvfVEtLDkCF~n-VcELDliF~~~k~h~iL~EiV~GGmVlETn~neIv~av~~ 143 (182)
T KOG0936|consen 80 SESELGILDLIQVFVETLDKCFEN-VCELDLIFNWQKVHAILAEIVMGGMVLETNMNEIVAAVDE 143 (182)
T ss_pred CcchhHHHHHHHHHHHHHHHHHHh-hhhhhheeeHHHHHHHHHHHHhCCeEEeccHHHHHHHHHH
Confidence 999999999999999999999999 9999999999999999999999999999999988777664
No 13
>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=99.44 E-value=3.8e-13 Score=113.36 Aligned_cols=139 Identities=14% Similarity=0.159 Sum_probs=124.1
Q ss_pred eeEEEEEEeCCCCEEEEEcccCCCCCc----------hHHHHHHhhcccccCCCCCeEEECCEEEEEEEeCcEEEEEEEc
Q 013709 4 AASAIYFLNLRGDVLINRLYRDDVGGN----------MVDAFRTHIMQTKELGTCPVRQIGGCSFFYMRISNVYIVIVVS 73 (438)
Q Consensus 4 mI~~i~Il~~~G~~l~~r~y~~~~~~~----------~~~~f~~~v~~~~~~~~~pi~~~~~~~~~~~~~~~l~~v~~~~ 73 (438)
.+.|++|+|++|++++.|||.+.+.+. ..+.|.+++.....+.+..|..+++...++.+..++.|..+..
T Consensus 7 ~v~a~LilDsqGeriy~kyy~pph~~eg~~~vFnsvkkekefek~l~eKt~k~~~~Il~f~d~lV~~k~~~dv~~yiv~~ 86 (187)
T COG5541 7 DVEALLILDSQGERIYRKYYQPPHRSEGHQLVFNSVKKEKEFEKKLAEKTAKDRESILMFYDRLVMCKRLDDVLLYIVSP 86 (187)
T ss_pred eeeeeEEecCCccchhhhhcCCcccccccchhhcchhHHHHHHHHHHHHhhcCccceeeEcceeeeeeeehhEEEEEecc
Confidence 578999999999999999999776532 3567888877554457888999999999999999999999999
Q ss_pred CCccHHHHHHHHHHHHHHHHhhcCCcCCHHHHHhhHHHHHHHHHHHHcCCeecccCHHHHhhhhhccCc
Q 013709 74 SNANVACAFKFVVEAVALFKSYFGGAFDEDAIRNNFVLIYELLDEIMDFGYPQNLSPEILKLYITQEGV 142 (438)
Q Consensus 74 ~~~n~~~~~~~L~~~~~vl~~y~~~~l~e~~i~~n~~~i~~lldE~id~G~p~~t~~~~l~~~i~~~~~ 142 (438)
-++|+.++.+.+..|...|.-.++...++..+.+||+.+..+.||.||.|.+.+|+++.+.++++.++.
T Consensus 87 meeNE~~l~q~f~~ir~Al~li~k~~~dkr~v~enYDqivl~vdEtid~Gvilet~s~~ia~rv~K~p~ 155 (187)
T COG5541 87 MEENEPFLGQVFDEIRAALILIVKTPTDKRNVWENYDQIVLLVDETIDEGVILETKSDEIADRVPKPPN 155 (187)
T ss_pred cccccHHHHHHHHHHHHHHHHHHcCCcchhhHHhhhceEEEeeehhcccceEeecChHHHHHhCCCCCC
Confidence 999999999999999999999999867788899999999999999999999999999999999998665
No 14
>PF10291 muHD: Muniscin C-terminal mu homology domain; InterPro: IPR018808 The muniscins are a family of endocytic adaptors that is conserved from yeast to humans.This C-terminal domain is structurally similar to mu homology domains, and is the region of the muniscin proteins involved in the interactions with the endocytic adaptor-scaffold proteins Ede1-eps15. This interaction influences muniscin localisation. The muniscins provide a combined adaptor-membrane-tubulation activity that is important for regulating endocytosis.; PDB: 3G9H_A.
Probab=99.16 E-value=1.3e-08 Score=97.30 Aligned_cols=228 Identities=18% Similarity=0.291 Sum_probs=124.1
Q ss_pred EEEEEEEeEEEEEecccceEEEEEEEEEEEEEeecC------CCeeEEEecCcccccccccccCCCCCCCceEeecccee
Q 013709 180 VFLDIVESVNLLMSSKGSVLRCDVTGKILMKCFLSG------MPDLKLGLNDKIGLEKESQLKSRPTKSGKTIELDDVTF 253 (438)
Q Consensus 180 i~vdV~E~l~~~~~~~G~i~~~~v~G~i~~~s~LsG------~P~~~l~ln~~~~~~~~~~~~~~~~~~~~~~~l~d~~f 253 (438)
+-.-|.|.|||.+. +|.+.++.|.|+|.+.---.- .+.+.+.|++... |+.+.-
T Consensus 3 l~asi~E~VnA~Fk-~g~~~~v~v~GEv~ls~~~~~~~~~~~~~~l~~rl~n~~~-------------------le~i~p 62 (257)
T PF10291_consen 3 LNASITETVNAYFK-GGQLSKVKVTGEVALSYPAGISSSLTSPPPLSFRLNNFSR-------------------LEKIAP 62 (257)
T ss_dssp EEEEEEEEEEEEEE-TTEEEEEEEEEEEEEEEE--SSS-----SEEEEEEETGGG-------------------EEEEEE
T ss_pred eeEEEEEEEEEEEE-CCcEEEEEEEEEEEEecCCChhhcccCCCcEEEEEcCcch-------------------hceeec
Confidence 45678999999997 788899999999998643322 3456777765422 121111
Q ss_pred eeeccccCccCcceEEEeCCC--CeE--EEEEEEecCC----CCCCeEEEEEEE-EcCceEEEEEEEEee-cCCCceeee
Q 013709 254 HQCVNLTRFNSEKTVSFVPPD--GEF--ELMKYRITEG----VNLPFRVLPTIK-ELGRTRMEVNVKIKS-VFGAKMFAL 323 (438)
Q Consensus 254 H~cV~~~~f~~~~~i~F~PPd--G~F--~Lm~Yr~~~~----~~~P~~v~~~~~-~~~~~~~e~~l~l~~-~~~~~~~~~ 323 (438)
.+..=...-.++....|.++- ... ..++|++... ...|+.+.+.-. +..+..+-+.+++.. .+.....++
T Consensus 63 N~~~v~~~~~~~~~f~~n~~~l~~~~~~~alKYqv~~~~~~~~~~Pl~l~~~Wk~e~~~tsl~l~Y~~Np~~~~~~~~L~ 142 (257)
T PF10291_consen 63 NPQFVSSSSQSDGEFWLNMSALTSHLPKQALKYQVHSDPSNLSSVPLILKPVWKCEPSQTSLILDYKLNPDAFASPVPLE 142 (257)
T ss_dssp -TTTE--EEEETTEEEE-TTTTBT-E-EEEEEEEEES--------SEEEEEEEEE-SSEEEEEEEEEE-TTT--E-EEEE
T ss_pred CHhHeecCCCCCCcEEEehHHhhhhhhhceEEEEEeccccccCCCCeEEEeEEEeCCceEEEEEEEEeChhhccccceee
Confidence 111000000112234443332 223 4699999753 568999987655 444455555555555 344456789
Q ss_pred eEEEEeeCCCC-CceeEEEEceeEEEEeccCcEEEEEeeecC--CCCe-eEEEEEEEeeccccccCCCCCCCeEEEEEeC
Q 013709 324 GVVIKIPVPKQ-TAKTSFQVTSGRAKYNASIDCLVWKIRKFP--GQTE-PTMSAEVELISTMAEKKSWTRPPIQMEFQVP 399 (438)
Q Consensus 324 ~v~i~ip~P~~-~~~~~~~~~~G~~~~~~~~~~i~W~I~k~~--g~~~-~~l~~~~~~~~~~~~~~~~~~~pi~v~F~i~ 399 (438)
||.|..++..+ ++++...+. | .|..+++.+.|+++.+. ++.+ ..|.|+|..... . ..-.+|.++|++.
T Consensus 143 nv~~~v~l~g~~~ts~~skP~-g--~~~~e~~ri~Wrl~el~~~~~~~~~kL~ARf~~~~~---~--~~p~~v~vkF~~~ 214 (257)
T PF10291_consen 143 NVVFSVPLDGGRATSAQSKPQ-G--TWNKEKNRITWRLPELSLTSEGEGGKLIARFMTSGG---P--SRPGGVEVKFEIE 214 (257)
T ss_dssp EEEEEEEB-SS-EEEEEESSS-----B-SSS-EEEEE-SSEEEETT---EEEEEEEEESS---------SS-EEEEEEE-
T ss_pred eEEEEEEcCCccccccccCCC-c--cccCCCcEEEEECCcccccCCCCCceEEEEEECCCC---C--CCCceEEEEEEEc
Confidence 99999999987 555554333 4 48899999999999864 3333 789999987654 1 1567899999999
Q ss_pred -cccccccEEEEEEEee-----cCCCcccccEEEEEecCcEEE
Q 013709 400 -MFTASGLRVRFLKVWE-----KSGYNTVEWVRYITKAGSYEI 436 (438)
Q Consensus 400 -~~t~SGl~V~~l~v~~-----~~~~~~~k~vrY~t~sg~Y~~ 436 (438)
+.+.||+.|.-+.-.+ ..+|+.. =++....||.|..
T Consensus 215 ~~~~~sg~~i~~~~~~~~~dp~~~~w~~~-~~~r~~~sGkY~~ 256 (257)
T PF10291_consen 215 GGSTLSGLGISLVYQDDEEDPPGGGWRLV-LVKRKLVSGKYIA 256 (257)
T ss_dssp --S-SS----EEEEEESSS-TT----EE--EEEEEEEEEEEE-
T ss_pred CCCcccCcEEEEeecccccCCCCCcceEE-EEEEEEeeeEEec
Confidence 8899999888772111 1134444 2555567899974
No 15
>PF03164 Mon1: Trafficking protein Mon1; InterPro: IPR004353 Members of this family have been called SAND proteins [] although these proteins do not contain a SAND domain. In Saccharomyces cerevisiae a protein complex of Mon1 and Ccz1 functions with the small GTPase Ypt7 to mediate vesicle trafficking to the vacuole [, ]. The Mon1/Ccz1 complex is conserved in eukaryotic evolution and members of this family (previously known as DUF254) are distant homologues to domains of known structure that assemble into cargo vesicle adapter (AP) complexes [, ].
Probab=95.01 E-value=0.17 Score=51.95 Aligned_cols=88 Identities=11% Similarity=0.111 Sum_probs=58.4
Q ss_pred EEEEEEeCCCCEEEEEcccCCCCC---chHHHHHHhhcccccCCCCCeEEECCEEEEEEEeCcEEEEEEEcCCccHHHHH
Q 013709 6 SAIYFLNLRGDVLINRLYRDDVGG---NMVDAFRTHIMQTKELGTCPVRQIGGCSFFYMRISNVYIVIVVSSNANVACAF 82 (438)
Q Consensus 6 ~~i~Il~~~G~~l~~r~y~~~~~~---~~~~~f~~~v~~~~~~~~~pi~~~~~~~~~~~~~~~l~~v~~~~~~~n~~~~~ 82 (438)
+.+||+++.||++.+|+=.++.-. +++.++..-+... ++.---+..++.++++..++.||+||+++.++++..+.
T Consensus 12 kh~fIlS~AGKPIysr~G~e~~l~~~~g~~~aiiS~~~~~--~d~l~~i~~~~~~ivfl~r~pl~lv~vS~~~e~~~~l~ 89 (415)
T PF03164_consen 12 KHFFILSSAGKPIYSRYGDEDKLSSLMGVIQAIISFFQSN--GDELRSIRAGDHRIVFLNRGPLILVAVSKTGESESQLR 89 (415)
T ss_pred CeEEEECCCCceeEEecCChHHHHHHHHHHHHHHHHHHhC--CCcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCHHHHH
Confidence 479999999999999972211111 1222222222111 22333567899999999999999999999988877766
Q ss_pred HHHHHHHHHHHhh
Q 013709 83 KFVVEAVALFKSY 95 (438)
Q Consensus 83 ~~L~~~~~vl~~y 95 (438)
.-|+.+...|-..
T Consensus 90 ~qL~~ly~qils~ 102 (415)
T PF03164_consen 90 KQLDYLYSQILSI 102 (415)
T ss_pred HHHHHHHHHHHHh
Confidence 6666655555544
No 16
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=94.22 E-value=0.28 Score=44.34 Aligned_cols=80 Identities=10% Similarity=0.080 Sum_probs=70.8
Q ss_pred EEEEEEEeCcEEEEEEEcCCccHHHHHHHHHHHHHHHHhhcCCcCCH-HHHHhhHHHHHHHHHHHHcCCeecccCHHHHh
Q 013709 56 CSFFYMRISNVYIVIVVSSNANVACAFKFVVEAVALFKSYFGGAFDE-DAIRNNFVLIYELLDEIMDFGYPQNLSPEILK 134 (438)
Q Consensus 56 ~~~~~~~~~~l~~v~~~~~~~n~~~~~~~L~~~~~vl~~y~~~~l~e-~~i~~n~~~i~~lldE~id~G~p~~t~~~~l~ 134 (438)
...++....++-|+.+++..+|.+++-.+|+.++..|.+.+.. ++. ..+...-+.|..+|+..++.|.-.-.+-..++
T Consensus 104 k~vvW~~v~~l~ftLVce~hEN~lLa~~~L~~~~~~l~~~~~~-l~~~~e~l~k~d~i~aiL~~fLP~GQLLFlN~~~~k 182 (189)
T PF15001_consen 104 KIVVWLGVGSLCFTLVCEPHENRLLAENTLRLFIRHLLEHLKI-LSQPSEVLLKSDRILAILHRFLPHGQLLFLNHRFVK 182 (189)
T ss_pred cEEEeeccCCEEEEEEecCchhHHHHHHHHHHHHHHHHHHHHH-hCcHHHhhhhHHHHHHHHHHhCCCCcEEEEcHHHHH
Confidence 5678899999999999999999999999999999999999966 543 67888999999999999999999888877666
Q ss_pred hh
Q 013709 135 LY 136 (438)
Q Consensus 135 ~~ 136 (438)
.+
T Consensus 183 ~l 184 (189)
T PF15001_consen 183 QL 184 (189)
T ss_pred HH
Confidence 54
No 17
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=94.04 E-value=1.1 Score=36.67 Aligned_cols=93 Identities=15% Similarity=0.238 Sum_probs=57.5
Q ss_pred ceeEEEEEEeCCCCEEEEEcccCCCC---Cc-------h---HHHHHHhhcccccCCCCCeEEECC-EEEEEEEeCcEEE
Q 013709 3 VAASAIYFLNLRGDVLINRLYRDDVG---GN-------M---VDAFRTHIMQTKELGTCPVRQIGG-CSFFYMRISNVYI 68 (438)
Q Consensus 3 ~mI~~i~Il~~~G~~l~~r~y~~~~~---~~-------~---~~~f~~~v~~~~~~~~~pi~~~~~-~~~~~~~~~~l~~ 68 (438)
|.+.++||+|+.|-.+..|.|..+.+ .+ . ..+...++........--++..+. +-++|+...++-|
T Consensus 1 mave~~~iINksGglifqref~~~et~lnsneyLiLastlhgV~aI~tq~~p~~gssg~~~l~~~~f~m~I~qT~TG~kF 80 (134)
T COG5122 1 MAVEQFFIINKSGGLIFQREFGEGETELNSNEYLILASTLHGVSAILTQTIPLPGSSGRLVLYFRNFVMTIFQTTTGTKF 80 (134)
T ss_pred CceeEEEEEecCCcEEEEEeccCCccccCcccEEEEeechhhhhhhhhhcccCCCCCceEEEEeccEEEEEEEecCCcEE
Confidence 67899999999999999999965433 11 1 111222222211111112445555 3457889999999
Q ss_pred EEEE-cCCccHHHHHHHHHHHHHHHHhhcCC
Q 013709 69 VIVV-SSNANVACAFKFVVEAVALFKSYFGG 98 (438)
Q Consensus 69 v~~~-~~~~n~~~~~~~L~~~~~vl~~y~~~ 98 (438)
|+++ +..+|.++- |+++.....+|.-+
T Consensus 81 V~~~~k~t~na~~q---l~kiY~lYsdYV~k 108 (134)
T COG5122 81 VFVAEKRTVNALFQ---LQKIYSLYSDYVTK 108 (134)
T ss_pred EEEecCCchhHHHH---HHHHHHHHHHHhhc
Confidence 9998 344454433 77788877777654
No 18
>PF08923 MAPKK1_Int: Mitogen-activated protein kinase kinase 1 interacting; InterPro: IPR015019 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry represents Mitogen-activated protein kinase kinase 1 interacting protein, which is a small subcellular adaptor protein required for MAPK signalling and ERK1/2 activation. The overall topology of this domain has a central five-stranded beta-sheet sandwiched between a two alpha-helix and a one alpha-helix layer []. ; PDB: 1VEU_A 1VET_A 1SKO_A 2ZL1_A 3CPT_A.
Probab=93.14 E-value=2.3 Score=35.66 Aligned_cols=90 Identities=17% Similarity=0.193 Sum_probs=61.6
Q ss_pred eEEEEEEeCCCCEEEEEcccCCCCCc-----hHHHHHHhhccccc---CCCCC-eEEECCEEEEEEEeCcEEEEEEEcCC
Q 013709 5 ASAIYFLNLRGDVLINRLYRDDVGGN-----MVDAFRTHIMQTKE---LGTCP-VRQIGGCSFFYMRISNVYIVIVVSSN 75 (438)
Q Consensus 5 I~~i~Il~~~G~~l~~r~y~~~~~~~-----~~~~f~~~v~~~~~---~~~~p-i~~~~~~~~~~~~~~~l~~v~~~~~~ 75 (438)
+.+|+|.|++|=+++.-. .+..+.. .+..|....-+.++ ++... +..++++..++.....+|+..+++.+
T Consensus 17 l~~I~itDrDGvpi~~v~-~~~~~~~~~~~~~~~tf~~a~~Q~~KL~lG~nk~ii~~Y~~~qvv~~~~~pl~it~ias~~ 95 (119)
T PF08923_consen 17 LQAIVITDRDGVPIAKVS-SDSAPESAMRPSLLSTFAMAIDQASKLGLGKNKSIIAYYDSYQVVQFNKLPLYITFIASSN 95 (119)
T ss_dssp EEEEEEEETTS-EEEEEE--TTS-GGGGSHHHHCCHHHHHHHHTTSSS-SEEEEEEEESSEEEEEEEETTEEEEEEEETT
T ss_pred eEEEEEECCCCcEEEEec-CCCCcchhhhhHHHHHHHHHhhcccccCCCCceEEEEEeCCEEEEEEeCCCeEEEEEecCC
Confidence 689999999998877633 3332321 22223222222211 33334 56899999999999999999999999
Q ss_pred ccHHHHHHHHHHHHHHHHhh
Q 013709 76 ANVACAFKFVVEAVALFKSY 95 (438)
Q Consensus 76 ~n~~~~~~~L~~~~~vl~~y 95 (438)
.|.-.++.+-+.+..++.+.
T Consensus 96 aN~G~il~l~~~L~~~l~~l 115 (119)
T PF08923_consen 96 ANTGLILSLEEELAPILNEL 115 (119)
T ss_dssp S-HHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHhHHHHHHHHHHH
Confidence 99999999999999988763
No 19
>PF04099 Sybindin: Sybindin-like family ; InterPro: IPR007233 Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses. Syndecan-2 induces spine formation by recruiting intracellular vesicles toward postsynaptic sites through the interaction with synbindin []. ; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005801 cis-Golgi network; PDB: 3CUE_C 2J3T_C 2ZMV_B 2JSN_A.
Probab=93.08 E-value=1.6 Score=37.86 Aligned_cols=91 Identities=12% Similarity=0.222 Sum_probs=55.8
Q ss_pred eEEEEEEeCCCCEEEEEcccCCC----CC---c----------hHHHHHHhhcccccC----CCC--CeEEECCEEE-EE
Q 013709 5 ASAIYFLNLRGDVLINRLYRDDV----GG---N----------MVDAFRTHIMQTKEL----GTC--PVRQIGGCSF-FY 60 (438)
Q Consensus 5 I~~i~Il~~~G~~l~~r~y~~~~----~~---~----------~~~~f~~~v~~~~~~----~~~--pi~~~~~~~~-~~ 60 (438)
|.+++|+|+.|..+.+|.|.... ++ + .+..|..++...... ... ..++++.++. +|
T Consensus 1 IyslyI~nr~G~lIy~~~~~~~~~~~~~~~~~ne~~ll~g~l~sl~~i~~klsp~~~~~~~~~~~g~~~~~T~~yklh~~ 80 (142)
T PF04099_consen 1 IYSLYIFNRSGGLIYYREWNRSKNEGQPKLSSNEYKLLAGMLHSLKAIASKLSPVDSKPNEPGSSGFESFETDTYKLHCF 80 (142)
T ss_dssp EEEEEEE-TTS-EEEEEETSSSS--E-SSSCHHHHHHHHHHHHHHHHHHHHT-SSSSSS-SSS--SEEEEEESS-EEEEE
T ss_pred CeEEEEEeCCcceeeehhhCCCCccccCCCChhHHHHHHhhHHHHHHHHHHhCCCCcccccccceeEEEEEeCCEEEEEE
Confidence 67999999999999999997643 11 1 134455554431110 011 2456677554 66
Q ss_pred EEeCcEEEEEEEcCCccHHHHHHHHHHHHHHHHhhc
Q 013709 61 MRISNVYIVIVVSSNANVACAFKFVVEAVALFKSYF 96 (438)
Q Consensus 61 ~~~~~l~~v~~~~~~~n~~~~~~~L~~~~~vl~~y~ 96 (438)
....++-||++|+.+.... .=++++.+.++.-+|.
T Consensus 81 eT~TGlKFvl~td~~~~~~-~~~l~~~~~~lY~dyV 115 (142)
T PF04099_consen 81 ETPTGLKFVLITDPNVPSL-RDELLRIYYELYVDYV 115 (142)
T ss_dssp E-TTS-EEEEEE-TTCCHC-HHHHHHHHHHHHHHHH
T ss_pred EcCcCcEEEEEecCCCccH-HHHHHHHHHHHHHHHH
Confidence 8889999999999988544 3347888888888875
No 20
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=89.98 E-value=3.9 Score=36.24 Aligned_cols=47 Identities=11% Similarity=0.203 Sum_probs=35.7
Q ss_pred eEEECC-EEEEEEEeCcEEEEEEEcCCccHHHHHHHHHHHHHHHHhhcCC
Q 013709 50 VRQIGG-CSFFYMRISNVYIVIVVSSNANVACAFKFVVEAVALFKSYFGG 98 (438)
Q Consensus 50 i~~~~~-~~~~~~~~~~l~~v~~~~~~~n~~~~~~~L~~~~~vl~~y~~~ 98 (438)
+++.+. ..++|+...++-||++++...+ .+=.+|+++.++..+|.=+
T Consensus 125 ~LetdtF~l~~~QTlTG~KFVvis~~~~~--~aD~lLrKiYelYsDyvlK 172 (199)
T KOG3369|consen 125 VLETDTFTLHIFQTLTGTKFVVIAEPGTQ--GADSLLRKIYELYSDYVLK 172 (199)
T ss_pred EEEeccEEEEEEEccCCcEEEEEecCCch--hHHHHHHHHHHHHHHHhhc
Confidence 566666 4568899999999999876652 3445889999999888643
No 21
>PF13774 Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3BW6_A 1H8M_A 3EGX_C 2NUP_C 3EGD_C 2NUT_C 3KYQ_A 1IFQ_B 2VX8_D ....
Probab=89.33 E-value=2.9 Score=32.39 Aligned_cols=50 Identities=18% Similarity=0.269 Sum_probs=43.6
Q ss_pred CCeEEECCEEEEEEEeCcEEEEEEEcCCccHHHHHHHHHHHHHHHHhhcC
Q 013709 48 CPVRQIGGCSFFYMRISNVYIVIVVSSNANVACAFKFVVEAVALFKSYFG 97 (438)
Q Consensus 48 ~pi~~~~~~~~~~~~~~~l~~v~~~~~~~n~~~~~~~L~~~~~vl~~y~~ 97 (438)
.-.++.++..|-+...+++.++|+|+.+-+.-.++.||..+.+-...-++
T Consensus 16 k~s~~~~~~~fh~~~~~~i~~~citd~~~~~r~aF~fL~~i~~~F~~~~~ 65 (83)
T PF13774_consen 16 KMSYESGNYVFHYLVEDGIAYLCITDKSYPKRVAFAFLEEIKQEFIQTYG 65 (83)
T ss_dssp EEEEEETTEEEEEEEETTEEEEEEEETTS-HHHHHHHHHHHHHHHHHHCT
T ss_pred eEEEEECCEEEEEEEcCCeEEEEEEcCCCCcchHHHHHHHHHHHHHHHcC
Confidence 34678899888888899999999999999999999999999999888777
No 22
>KOG0997 consensus Uncharacterized conserved protein Sand [Function unknown]
Probab=88.57 E-value=1.8 Score=44.32 Aligned_cols=86 Identities=13% Similarity=0.154 Sum_probs=55.4
Q ss_pred EEEEEEeCCCCEEEEEcccCCCC---CchHHHHHHhhcccccCCCCCeEEECCEEEEEEEeCcEEEEEEEcCCccHHHH-
Q 013709 6 SAIYFLNLRGDVLINRLYRDDVG---GNMVDAFRTHIMQTKELGTCPVRQIGGCSFFYMRISNVYIVIVVSSNANVACA- 81 (438)
Q Consensus 6 ~~i~Il~~~G~~l~~r~y~~~~~---~~~~~~f~~~v~~~~~~~~~pi~~~~~~~~~~~~~~~l~~v~~~~~~~n~~~~- 81 (438)
+.+||+++.|+++++|+-..+.- -++..+...-+-.. +..-..+..+|..+++.+.+-|++||+++.+..+...
T Consensus 118 khifilseaGKPiyS~~gs~e~l~stmGv~~alISf~q~~--~~~i~si~a~g~k~vfl~kspl~LvA~s~t~~Sa~qL~ 195 (523)
T KOG0997|consen 118 KHIFILSEAGKPIYSRHGSDEALSSTMGVMQALISFFQVS--GLAITSIHAFGNKLVFLQKSPLLLVAVSRTSQSAAQLL 195 (523)
T ss_pred ceEEEEecCCCceeeecCcHHHHHHHHHHHHHHHHHHhhC--CceEEEEEecCceEEEEecCcEEEEEEcccccCHHHHH
Confidence 36899999999999998553322 12222222111111 2344577889999999999999999999877766543
Q ss_pred HHHHHHHHHHHH
Q 013709 82 FKFVVEAVALFK 93 (438)
Q Consensus 82 ~~~L~~~~~vl~ 93 (438)
.+++....++|.
T Consensus 196 ~qL~~ly~QIlS 207 (523)
T KOG0997|consen 196 QQLLLLYCQILS 207 (523)
T ss_pred HHHHHHHHHHHH
Confidence 333344444444
No 23
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=85.88 E-value=9.9 Score=32.18 Aligned_cols=84 Identities=11% Similarity=0.145 Sum_probs=50.0
Q ss_pred ceeEEEEEEeCCCCEEEEEcccCCCCC-----ch----------HHHHHHhhcccccCCCCCeEEE--CCEEE-EEEEeC
Q 013709 3 VAASAIYFLNLRGDVLINRLYRDDVGG-----NM----------VDAFRTHIMQTKELGTCPVRQI--GGCSF-FYMRIS 64 (438)
Q Consensus 3 ~mI~~i~Il~~~G~~l~~r~y~~~~~~-----~~----------~~~f~~~v~~~~~~~~~pi~~~--~~~~~-~~~~~~ 64 (438)
|.|.+++|+|+.|..|.++.|...... .. +..|-.++...+ ....+..+ ..+.. .|-.-.
T Consensus 1 Mtiy~~yIFdR~g~Cl~y~EW~r~~~s~~~~eee~KL~yGmlFSlkS~v~Kls~~d--~k~~f~sy~Ts~YklhfyeTpt 78 (140)
T KOG3368|consen 1 MTIYNFYIFDRNGVCLFYREWNRTKQSGIPNEEEAKLMYGMLFSLKSFVSKLSPGD--VKDGFLSYKTSKYKLHFYETPT 78 (140)
T ss_pred CeEEEEEEEcCCccEEEehhcccccccCCchhHHHHHHHHHHhhHHHHHHhcCCCC--cccCeeEEeeceeEEEEEEcCC
Confidence 789999999999999999988533221 11 233443433221 12223333 33333 234558
Q ss_pred cEEEEEEEcCCccHHHHHHHHHHHHH
Q 013709 65 NVYIVIVVSSNANVACAFKFVVEAVA 90 (438)
Q Consensus 65 ~l~~v~~~~~~~n~~~~~~~L~~~~~ 90 (438)
+|.||..|+.+... +-+.||.|..
T Consensus 79 glk~vl~Tdpk~~~--ir~vLq~IYs 102 (140)
T KOG3368|consen 79 GLKFVLNTDPKAGS--IRDVLQYIYS 102 (140)
T ss_pred CcEEEEecCCCccc--HHHHHHHHHH
Confidence 89999999877544 3455666666
No 24
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=83.58 E-value=30 Score=31.48 Aligned_cols=85 Identities=16% Similarity=0.278 Sum_probs=61.2
Q ss_pred eCCCCEEEEEcc--cCCCCCchHHHHHHhhcccccCCCCCeEEECCEEEEEEEeCcEEEEEEEcCCccHHHHHHHHHHHH
Q 013709 12 NLRGDVLINRLY--RDDVGGNMVDAFRTHIMQTKELGTCPVRQIGGCSFFYMRISNVYIVIVVSSNANVACAFKFVVEAV 89 (438)
Q Consensus 12 ~~~G~~l~~r~y--~~~~~~~~~~~f~~~v~~~~~~~~~pi~~~~~~~~~~~~~~~l~~v~~~~~~~n~~~~~~~L~~~~ 89 (438)
=.+|-++++++= .+. ..++.+....++-.. ++..--...|++.|-|...+++.++|+++...--...+.||.++.
T Consensus 8 VARGTvvLaeft~~~gN-f~sva~qiL~klp~~--~n~k~tYs~d~y~Fh~l~~dg~tylcvadds~gR~ipfaFLe~Ik 84 (217)
T KOG0859|consen 8 VARGTVILAEFTEFSGN-FSSIAAQILQKLPSS--SNSKFTYSCDGYTFHYLVEDGLTYLCVADDSAGRQIPFAFLERIK 84 (217)
T ss_pred EecceEEEEeeeeccCC-HHHHHHHHHHhCCCC--CCCceEEecCCeEEEEEEeCCeEEEEEEeccccccccHHHHHHHH
Confidence 358999999862 111 123444444443322 233456788999999999999999999998888788999999999
Q ss_pred HHHHhhcCCc
Q 013709 90 ALFKSYFGGA 99 (438)
Q Consensus 90 ~vl~~y~~~~ 99 (438)
+-+..-.|..
T Consensus 85 ~~F~k~YG~~ 94 (217)
T KOG0859|consen 85 EDFKKRYGGG 94 (217)
T ss_pred HHHHHHhccc
Confidence 9887777763
No 25
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=82.27 E-value=17 Score=37.75 Aligned_cols=112 Identities=14% Similarity=0.095 Sum_probs=72.7
Q ss_pred eeEEEEEEeCCCCEEEEEcccCCCCCchHHHHHHhhc-ccccCCCCCeEEECCEEEEEEEeCc--EEEEEEEcCCccHHH
Q 013709 4 AASAIYFLNLRGDVLINRLYRDDVGGNMVDAFRTHIM-QTKELGTCPVRQIGGCSFFYMRISN--VYIVIVVSSNANVAC 80 (438)
Q Consensus 4 mI~~i~Il~~~G~~l~~r~y~~~~~~~~~~~f~~~v~-~~~~~~~~pi~~~~~~~~~~~~~~~--l~~v~~~~~~~n~~~ 80 (438)
||..|.|+++.|-+|...+=-+......+..|.+.++ ....+... +..+.++.=|...++ +.|+++-..-.+-..
T Consensus 1 Mld~faIFtkgG~vLw~~~~~~~~~~~~in~lI~~~ll~er~~~~~--~~~~~yTlk~q~~N~~~lvfvvvfqki~~L~y 78 (587)
T KOG0781|consen 1 MLDQFAIFTKGGLVLWCYQEVGDNLKGPINALIRSVLLSERGGVNS--FTFEAYTLKYQLDNQYSLVFVVVFQKILTLTY 78 (587)
T ss_pred CcceeeeecCCcEEEEEecccchhccchHHHHHHHHHHHhhcCccc--CchhheeEeeeecCCccEEEEEEEeccchhhh
Confidence 8999999999998886654333333445566655555 32222222 566666666666655 666777666666667
Q ss_pred HHHHHHHHHHHHHhhcCCcCCHHHHHhhHHH-HHHHHHH
Q 013709 81 AFKFVVEAVALFKSYFGGAFDEDAIRNNFVL-IYELLDE 118 (438)
Q Consensus 81 ~~~~L~~~~~vl~~y~~~~l~e~~i~~n~~~-i~~lldE 118 (438)
+-.+|....+.+.+-++. .+-..++.|++. -.++|++
T Consensus 79 v~~ll~~v~~~f~e~~~~-~~~~~l~~n~~~~~~e~lk~ 116 (587)
T KOG0781|consen 79 VDKLLNDVLNLFREKYDT-QSALSLLNNTFDFQEELLKL 116 (587)
T ss_pred HHHHHHHHHHHHHHHhcc-chHHHhhhhhHHHHHHHHHH
Confidence 777888888888777776 777778888754 4444443
No 26
>PF09201 SRX: SRX; InterPro: IPR015284 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. This entry represents a homologue of the alpha subunit of the SR receptor. Members of this entry consist of a central six-stranded anti-parallel beta-sheet sandwiched by helix alpha1 on one side and helices alpha2-alpha4 on the other. They interact with the small GTPase SR-beta, forming a complex that matches a class of small G protein-effector complexes, including Rap-Raf, Ras-PI3K(gamma), Ras-RalGDS, and Arl2-PDE(delta) []. ; PDB: 1NRJ_A.
Probab=73.03 E-value=23 Score=30.34 Aligned_cols=71 Identities=14% Similarity=0.258 Sum_probs=37.5
Q ss_pred eeEEEEEEeCCCCEEEEEcccC-CCCCchHHHHHHhhccccc-----CCCCCeEEEC-------CEEEEEE--EeCcEEE
Q 013709 4 AASAIYFLNLRGDVLINRLYRD-DVGGNMVDAFRTHIMQTKE-----LGTCPVRQIG-------GCSFFYM--RISNVYI 68 (438)
Q Consensus 4 mI~~i~Il~~~G~~l~~r~y~~-~~~~~~~~~f~~~v~~~~~-----~~~~pi~~~~-------~~~~~~~--~~~~l~~ 68 (438)
|+.++.|++..|++|..-.=-+ ......+..|..+++..+- +...-+..+. +..+.|. +.-.|||
T Consensus 1 MfdQlaIFTpqGqvLyqyN~~gKKFsE~QiN~FIs~lItsP~~~~e~~~~~k~~~i~s~~~~~~~f~~mfh~sKQPeLy~ 80 (148)
T PF09201_consen 1 MFDQLAIFTPQGQVLYQYNCLGKKFSETQINAFISHLITSPVTKKEDSSKSKFLTISSEKKNSRSFSAMFHISKQPELYY 80 (148)
T ss_dssp ---EEEEE-TT-BEEEEEETTS----HHHHHHHHHHHHHS---GGGTT--EEEEE-----------EEEEEEETTTTEEE
T ss_pred CcceeEEeccCceEEEEecccchHHHHHHHHHHHHHHhcCCCcccCCCcceeeEEecccccCCCChheeeeecCCCcEEE
Confidence 8999999999999997754222 2224567788888885432 1122344443 5555543 4577999
Q ss_pred EEEEcC
Q 013709 69 VIVVSS 74 (438)
Q Consensus 69 v~~~~~ 74 (438)
|++-..
T Consensus 81 VvTyae 86 (148)
T PF09201_consen 81 VVTYAE 86 (148)
T ss_dssp EEEESS
T ss_pred EEEecc
Confidence 988654
No 27
>PF00235 Profilin: Profilin; InterPro: IPR002097 Profilin is a small eukaryotic protein that binds to monomeric actin (G-actin) in a 1:1 ratio thus preventing the polymerisation of actin into filaments (F-actin). It can also in certain circumstance promote actin polymerisation. Profilin also binds to polyphosphoinositides such as PIP2. Overall sequence similarity among profilin from organisms which belong to different phyla (ranging from fungi to mammals) is low, but the N-terminal region is relatively well conserved. That region is thought to be involved in the binding to actin. A protein structurally similar to profilin is present in the genome of Variola virus and Vaccinia virus (gene A42R). Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Ara t 8, Bet v 2, Cyn d 12, Hel a 2, Mer a 1 and Phl p 11.; GO: 0003779 actin binding, 0007010 cytoskeleton organization, 0015629 actin cytoskeleton; PDB: 1ACF_A 3NEC_C 2V8F_B 2V8C_A 2VK3_A 2JKF_A 2JKG_A 1F2K_B 2ACG_A 1YPR_B ....
Probab=47.25 E-value=1.6e+02 Score=24.17 Aligned_cols=87 Identities=8% Similarity=0.074 Sum_probs=47.4
Q ss_pred eEEEEEEeCCCCEEEEEcccCCCCCchHHHHHHhhcccccCCCCCeEEECCEEEEEE-------------------EeCc
Q 013709 5 ASAIYFLNLRGDVLINRLYRDDVGGNMVDAFRTHIMQTKELGTCPVRQIGGCSFFYM-------------------RISN 65 (438)
Q Consensus 5 I~~i~Il~~~G~~l~~r~y~~~~~~~~~~~f~~~v~~~~~~~~~pi~~~~~~~~~~~-------------------~~~~ 65 (438)
+.+..|++.+|.+..+.---...+...+..+...+..... ....-|.++|.+|... +.+.
T Consensus 16 ~~~aaI~~~dG~vwA~s~~f~~~~~~E~~~i~~~f~~~~~-~~~~gi~l~G~kY~~~~~d~~~i~~k~~~~G~~i~kt~~ 94 (121)
T PF00235_consen 16 ITKAAIIGSDGSVWASSPGFSNISPEEAKAIIKAFNNPSK-FPSNGITLGGKKYIVLRADDNSIYGKKGKGGIIIVKTKQ 94 (121)
T ss_dssp ESEEEEEETTSSEEEEETTGGGCSHHHHHHHHHHHHSSSH-HHHH-EEETTEEEEEEEEETTEEEEEETTEEEEEEECSS
T ss_pred EeEEEEEcCCCCEEEecCCCCCCCHHHHHHHHHHhcCchh-cccCCeEEcCcEeEEEecCCceEEeeCCCCcEEEEECCC
Confidence 5677888999987775542101222222233222121110 1112345555555443 3345
Q ss_pred EEEEEEEcCCccHHHHHHHHHHHHHHH
Q 013709 66 VYIVIVVSSNANVACAFKFVVEAVALF 92 (438)
Q Consensus 66 l~~v~~~~~~~n~~~~~~~L~~~~~vl 92 (438)
.++|+....+.++-.......++++.|
T Consensus 95 ~ivIg~y~~~~~~~~~~~~v~~lA~yL 121 (121)
T PF00235_consen 95 AIVIGMYDESIQPGNCNKAVEKLADYL 121 (121)
T ss_dssp EEEEEEEETTSTHHHHHHHHHHHHHHH
T ss_pred EEEEEEeCCCCCHHHHHHHHHHHHhhC
Confidence 667777777788888888888887765
No 28
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=46.86 E-value=2.4e+02 Score=26.16 Aligned_cols=49 Identities=16% Similarity=0.323 Sum_probs=43.7
Q ss_pred eEEECCEEEEEEEeCcEEEEEEEcCCccHHHHHHHHHHHHHHHHhhcCC
Q 013709 50 VRQIGGCSFFYMRISNVYIVIVVSSNANVACAFKFVVEAVALFKSYFGG 98 (438)
Q Consensus 50 i~~~~~~~~~~~~~~~l~~v~~~~~~~n~~~~~~~L~~~~~vl~~y~~~ 98 (438)
-++.+++.|-|.-.+++.+.++++.+-+--+++.+|+.+.+-+..-.+.
T Consensus 53 Sietg~f~fHfli~~~Vcylvicd~~yP~kLAF~YLedL~~EF~~~~~~ 101 (216)
T KOG0862|consen 53 SIETGPFVFHFLIESGVCYLVICDKSYPRKLAFSYLEDLAQEFDKSYGK 101 (216)
T ss_pred ccccCCeEEEEEecCCEEEEEEecCCCcHHHHHHHHHHHHHHHHHhccc
Confidence 5677889999999999999999999999999999999999988777765
No 29
>PF04628 Sedlin_N: Sedlin, N-terminal conserved region; InterPro: IPR006722 Sedlin is a 140 amino-acid protein with a putative role in endoplasmic reticulum-to-Golgi transport. Several missense mutations and deletion mutations in the SEDL gene, which result in protein truncation by frame shift, are responsible for spondyloepiphyseal dysplasia tarda, a progressive skeletal disorder (OMIM:313400). [].; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005622 intracellular; PDB: 3PR6_A 2J3W_A 1H3Q_A.
Probab=37.28 E-value=2.5e+02 Score=23.68 Aligned_cols=90 Identities=10% Similarity=0.158 Sum_probs=50.7
Q ss_pred EEeCCCCEEEEEcccCCCCCc--------------hHHHHHHhhcc-cccCCCCCeEEECC-EEEEEEEeCcEEEEEEEc
Q 013709 10 FLNLRGDVLINRLYRDDVGGN--------------MVDAFRTHIMQ-TKELGTCPVRQIGG-CSFFYMRISNVYIVIVVS 73 (438)
Q Consensus 10 Il~~~G~~l~~r~y~~~~~~~--------------~~~~f~~~v~~-~~~~~~~pi~~~~~-~~~~~~~~~~l~~v~~~~ 73 (438)
|++++.++|+.+.|....... .+|.|...+.. ..+..-.-+...++ ..|.|+.-.++-|+++.+
T Consensus 1 IIg~~n~PLy~~~~~~~~~~~~~~~~~l~~~~~h~sLD~iee~~~~~~~~~yLg~l~~~~~~~vygyvT~t~~Kfvl~~~ 80 (132)
T PF04628_consen 1 IIGPNNNPLYIRSFPSEKESSSSDARHLYQFIAHSSLDVIEEKLWKSSSDMYLGLLDPFEDYKVYGYVTNTGIKFVLVHD 80 (132)
T ss_dssp EE-TTS-EEEEEEE--ST-CGHHHHHHHHHHHHHHHHHHHHHCCHCSSSCSEEEEEEEETTEEEEEEETTT--EEEEEEC
T ss_pred CCCCCCcceEEEecCCCcccccchHHHHHHHHHHHHHHHHHHHHhhcccccccCceehhhhHHHHhhhccCceeEEEEEe
Confidence 678999999999997654432 34555444443 11111123445566 557888889999999987
Q ss_pred ---CCccHHHHHHHHHHHHHHHHhhcCCc
Q 013709 74 ---SNANVACAFKFVVEAVALFKSYFGGA 99 (438)
Q Consensus 74 ---~~~n~~~~~~~L~~~~~vl~~y~~~~ 99 (438)
...+.-.+-.|++++.++.-+++-++
T Consensus 81 ~~~~~~~d~~ik~fF~~vh~~Y~~~~~NP 109 (132)
T PF04628_consen 81 MSDNSIRDEDIKQFFKEVHELYVKALCNP 109 (132)
T ss_dssp GGG-S--HHHHHHHHHHHHHHHHHHHTST
T ss_pred cccCCcchHHHHHHHHHHHHHHHHHccCC
Confidence 33455566677777777766666655
No 30
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=33.18 E-value=67 Score=25.69 Aligned_cols=19 Identities=16% Similarity=0.011 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHcCCeeccc
Q 013709 110 VLIYELLDEIMDFGYPQNL 128 (438)
Q Consensus 110 ~~i~~lldE~id~G~p~~t 128 (438)
..|..+++++++.|++..|
T Consensus 80 ~~v~~al~~L~~eG~IYsT 98 (102)
T PF08784_consen 80 NEVRKALDFLSNEGHIYST 98 (102)
T ss_dssp HHHHHHHHHHHHTTSEEES
T ss_pred HHHHHHHHHHHhCCeEecc
Confidence 4567999999999999876
No 31
>KOG0861 consensus SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.41 E-value=3.6e+02 Score=24.24 Aligned_cols=91 Identities=12% Similarity=0.142 Sum_probs=48.5
Q ss_pred ceeEEEEEEeCCCCE--EEEEccc----CCCCCchHHHH---H-Hhhccccc-CCCCCeEEECCEEEEEEEeCcEEEEEE
Q 013709 3 VAASAIYFLNLRGDV--LINRLYR----DDVGGNMVDAF---R-THIMQTKE-LGTCPVRQIGGCSFFYMRISNVYIVIV 71 (438)
Q Consensus 3 ~mI~~i~Il~~~G~~--l~~r~y~----~~~~~~~~~~f---~-~~v~~~~~-~~~~pi~~~~~~~~~~~~~~~l~~v~~ 71 (438)
|-|.++.|+...+.. ++...+. +-..|+...+| . +.+..+.. +....+=+-+-...+|.+-++|--|++
T Consensus 1 Mki~sl~V~~~~~~~~~ll~~a~dls~FsfFqRssV~Efm~F~sktvaeRt~~g~rqsvk~~~Y~~h~yvrndgL~~V~~ 80 (198)
T KOG0861|consen 1 MKIYSLSVLHKGTSDVKLLKTASDLSSFSFFQRSSVQEFMTFISKTVAERTGPGQRQSVKHEEYLVHVYVRNDGLCGVLI 80 (198)
T ss_pred CceEEEEEEeeCCcchhhhhhhcccccccceeeccHHHHHHHHHHHHHHhcCcccccccccceeEEEEEEecCCeeEEEE
Confidence 568889999885533 2222221 01224544444 2 23333322 222222222223457778889999999
Q ss_pred EcCCccHHHHHHHHHHHHHHHHhhc
Q 013709 72 VSSNANVACAFKFVVEAVALFKSYF 96 (438)
Q Consensus 72 ~~~~~n~~~~~~~L~~~~~vl~~y~ 96 (438)
++.+-.--.++.+|++ +|++|.
T Consensus 81 ~D~eYP~rvA~tLL~k---vld~~~ 102 (198)
T KOG0861|consen 81 ADDEYPVRVAFTLLNK---VLDEFT 102 (198)
T ss_pred ecCcCchhHHHHHHHH---HHHHHh
Confidence 9877666666666654 455553
No 32
>PF03504 Chlam_OMP6: Chlamydia cysteine-rich outer membrane protein 6; InterPro: IPR003506 Three cysteine-rich proteins (also believed to be lipoproteins) make up the extracellular matrix of the Chlamydial outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. As these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism. The largest of these is the major outer membrane protein (MOMP), and constitutes around 60% of the total protein for the membrane []. OMP6 is the second largest, with a molecular mass of 58kDa, while the OMP3 protein is ~15kDa []. MOMP is believed to elicit the strongest immune response, and has recently been linked to heart disease through its sequence similarity to a murine heart-muscle specific alpha myosin []. The OMP6 family plays a structural role in the outer membrane during the EB stage of the Chlamydial cell, and different biovars show a small, yet highly significant, change at peptide charge level []. Members of this family include Chlamydia trachomatis, Chlamydia pneumoniae and Chlamydia psittaci.; GO: 0005201 extracellular matrix structural constituent
Probab=28.43 E-value=2.9e+02 Score=21.57 Aligned_cols=43 Identities=23% Similarity=0.332 Sum_probs=27.5
Q ss_pred eeeeEEEEeeCCCCCceeEEEEceeEEEEeccCcEEEEEeeecCCCC
Q 013709 321 FALGVVIKIPVPKQTAKTSFQVTSGRAKYNASIDCLVWKIRKFPGQT 367 (438)
Q Consensus 321 ~~~~v~i~ip~P~~~~~~~~~~~~G~~~~~~~~~~i~W~I~k~~g~~ 367 (438)
.+-||.|+=.+|-.+. +-.+.-.++ -...+.++|+|+.+..+.
T Consensus 43 DcvnVviTqqLPce~e---FV~SdPett-p~~D~kLVW~Ig~l~~G~ 85 (95)
T PF03504_consen 43 DCVNVVITQQLPCEVE---FVRSDPETT-PTPDGKLVWKIGRLGQGE 85 (95)
T ss_pred ceeEEEEeecCCcceE---EEecCCccc-cCCCCEEEEEeccccCCc
Confidence 4778999999997633 222222221 124678999999986555
No 33
>PF13598 DUF4139: Domain of unknown function (DUF4139)
Probab=27.63 E-value=5.7e+02 Score=24.79 Aligned_cols=108 Identities=19% Similarity=0.373 Sum_probs=59.5
Q ss_pred CccCcceEEEeCCCCeEEEEEEEecCCCCCCeEEEEEEEE-------cC---ceEEEEEEEEeecCCCceeeeeEEEEee
Q 013709 261 RFNSEKTVSFVPPDGEFELMKYRITEGVNLPFRVLPTIKE-------LG---RTRMEVNVKIKSVFGAKMFALGVVIKIP 330 (438)
Q Consensus 261 ~f~~~~~i~F~PPdG~F~Lm~Yr~~~~~~~P~~v~~~~~~-------~~---~~~~e~~l~l~~~~~~~~~~~~v~i~ip 330 (438)
.|-.+..|.+++|+++|.| .+-.+. -++|...... .+ ....++++.++...+. .-.|.|.=+
T Consensus 194 ~~vG~~~l~~~~~ge~~~l-~~G~d~----~v~v~r~~~~~~~~~g~~~~~~~~~~~~~itv~N~~~~---~v~v~v~d~ 265 (317)
T PF13598_consen 194 TFVGESRLPHTAPGEEFEL-SFGVDP----DVRVERKLLKKEEERGFFGKSQRRTYEYTITVRNNKDE---PVTVTVEDQ 265 (317)
T ss_pred EEEEeeecCCCCCCCEEEE-EcccCC----CEEEEEEecceecccccccccEEEEEEEEEEEECCCCC---CEEEEEEeC
Confidence 4555678999999999974 344332 2333322211 11 1234555666654432 334777767
Q ss_pred CCCCC-ceeEEEEce-eEEEEeccCcEEEEEeeecCCCCeeEEEEEEEe
Q 013709 331 VPKQT-AKTSFQVTS-GRAKYNASIDCLVWKIRKFPGQTEPTMSAEVEL 377 (438)
Q Consensus 331 ~P~~~-~~~~~~~~~-G~~~~~~~~~~i~W~I~k~~g~~~~~l~~~~~~ 377 (438)
+|-.. ..++++... .....+...+.+.|++.-=+|++ .+|+..+++
T Consensus 266 iPvs~~~~I~V~~~~~~~~~~~~~~g~~~W~~~l~~g~~-~~l~~~y~v 313 (317)
T PF13598_consen 266 IPVSEDEDIKVELLEPPEPNEDEKDGILEWKVTLPPGES-RTLEFSYEV 313 (317)
T ss_pred CCCCCCceEEEEEcCCCCCcccCCCCEEEEEEEECCCCE-EEEEEEEEE
Confidence 77543 233333222 12245678899999999766554 455555544
No 34
>PRK09750 hypothetical protein; Provisional
Probab=23.97 E-value=59 Score=23.48 Aligned_cols=14 Identities=43% Similarity=0.857 Sum_probs=11.4
Q ss_pred ecCCCcccccEEEE
Q 013709 415 EKSGYNTVEWVRYI 428 (438)
Q Consensus 415 ~~~~~~~~k~vrY~ 428 (438)
++.+..|.+|+||.
T Consensus 11 ~KpGg~P~~W~r~s 24 (64)
T PRK09750 11 EKEGGTPTNWTRYS 24 (64)
T ss_pred ECCCCCccceeEec
Confidence 55677899999995
No 35
>TIGR01451 B_ant_repeat conserved repeat domain. This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins.
Probab=23.74 E-value=2.6e+02 Score=19.48 Aligned_cols=31 Identities=16% Similarity=0.178 Sum_probs=24.5
Q ss_pred eEEEEEEEEeecCCCceeeeeEEEEeeCCCCCc
Q 013709 304 TRMEVNVKIKSVFGAKMFALGVVIKIPVPKQTA 336 (438)
Q Consensus 304 ~~~e~~l~l~~~~~~~~~~~~v~i~ip~P~~~~ 336 (438)
..++|++.++..-+ ..+.+|.|.=++|.+..
T Consensus 12 d~v~Yti~v~N~g~--~~a~~v~v~D~lP~g~~ 42 (53)
T TIGR01451 12 DTITYTITVTNNGN--VPATNVVVTDILPSGTT 42 (53)
T ss_pred CEEEEEEEEEECCC--CceEeEEEEEcCCCCCE
Confidence 47899998887644 35789999999998744
No 36
>PF07151 DUF1391: Protein of unknown function (DUF1391); InterPro: IPR009821 This family consists of several Enterobacterial proteins of around 50 residues in length. Members of this family are found in Escherichia coli and Salmonella typhi where they are often known as YdfA. The function of this family is unknown.
Probab=20.99 E-value=1.1e+02 Score=20.62 Aligned_cols=17 Identities=35% Similarity=0.659 Sum_probs=13.5
Q ss_pred EeCCCCeEEEEEEEecC
Q 013709 270 FVPPDGEFELMKYRITE 286 (438)
Q Consensus 270 F~PPdG~F~Lm~Yr~~~ 286 (438)
|---||.|+.|.|.-+.
T Consensus 16 fpn~dgtftamtytksk 32 (49)
T PF07151_consen 16 FPNQDGTFTAMTYTKSK 32 (49)
T ss_pred eeCCCCcEEEEEEeecc
Confidence 44568999999998753
No 37
>KOG0647 consensus mRNA export protein (contains WD40 repeats) [RNA processing and modification]
Probab=20.18 E-value=2.8e+02 Score=27.31 Aligned_cols=88 Identities=15% Similarity=0.222 Sum_probs=58.7
Q ss_pred EEeEEEEEecccceEEEEEEEEEEEEEeecCCCeeEEEecCcccccccccccCCCCCCCceEeeccceeeeeccccCc--
Q 013709 185 VESVNLLMSSKGSVLRCDVTGKILMKCFLSGMPDLKLGLNDKIGLEKESQLKSRPTKSGKTIELDDVTFHQCVNLTRF-- 262 (438)
Q Consensus 185 ~E~l~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~~~~~~l~d~~fH~cV~~~~f-- 262 (438)
+-.|.+..+++|. .-..|.|.+.++.--.|+|.-.+.|.-...-+ + ....---+.++.||| | -..|
T Consensus 201 ~R~va~f~d~~~~-alGsiEGrv~iq~id~~~~~~nFtFkCHR~~~--------~-~~~~VYaVNsi~FhP-~-hgtlvT 268 (347)
T KOG0647|consen 201 TRCVACFQDKDGF-ALGSIEGRVAIQYIDDPNPKDNFTFKCHRSTN--------S-VNDDVYAVNSIAFHP-V-HGTLVT 268 (347)
T ss_pred eeEEEEEecCCce-EeeeecceEEEEecCCCCccCceeEEEeccCC--------C-CCCceEEecceEeec-c-cceEEE
Confidence 3456777788887 77899999999999999998888886542111 0 111123467889999 3 2233
Q ss_pred -cCcceEEEeCCCCeEEEEEEEe
Q 013709 263 -NSEKTVSFVPPDGEFELMKYRI 284 (438)
Q Consensus 263 -~~~~~i~F~PPdG~F~Lm~Yr~ 284 (438)
.+|.+.+|-.-|.+-.|..|..
T Consensus 269 aGsDGtf~FWDkdar~kLk~s~~ 291 (347)
T KOG0647|consen 269 AGSDGTFSFWDKDARTKLKTSET 291 (347)
T ss_pred ecCCceEEEecchhhhhhhccCc
Confidence 3466777777777666766654
Done!