Query 014251
Match_columns 428
No_of_seqs 162 out of 1282
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 03:19:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014251.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014251hhsearch_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 7E-103 1E-107 724.7 38.3 417 4-426 1-446 (446)
2 KOG0937 Adaptor complexes medi 100.0 9.2E-91 2E-95 673.0 41.8 422 5-427 1-424 (424)
3 KOG2740 Clathrin-associated pr 100.0 1.8E-77 3.8E-82 560.7 33.9 402 4-427 1-418 (418)
4 PF00928 Adap_comp_sub: Adapto 100.0 3.5E-60 7.5E-65 454.6 29.7 261 159-427 1-262 (262)
5 KOG2635 Medium subunit of clat 100.0 2.6E-37 5.6E-42 296.7 35.6 366 3-403 1-490 (512)
6 KOG2677 Stoned B synaptic vesi 100.0 2.1E-36 4.4E-41 300.6 8.2 255 165-426 581-890 (922)
7 PF01217 Clat_adaptor_s: Clath 100.0 3.8E-27 8.3E-32 204.6 17.1 135 4-141 1-138 (141)
8 COG5030 APS2 Clathrin adaptor 99.9 9.3E-21 2E-25 155.7 12.7 133 4-139 1-136 (152)
9 KOG3343 Vesicle coat complex C 99.8 1.3E-18 2.9E-23 146.2 13.9 138 5-144 9-149 (175)
10 KOG0935 Clathrin adaptor compl 99.8 1.1E-18 2.5E-23 139.5 10.8 134 4-139 1-137 (143)
11 KOG0934 Clathrin adaptor compl 99.8 1.9E-19 4.1E-24 147.9 6.4 128 4-134 1-131 (145)
12 KOG0936 Clathrin adaptor compl 99.7 3.3E-17 7E-22 136.6 12.7 156 4-162 1-165 (182)
13 COG5541 RET3 Vesicle coat comp 99.4 9.8E-13 2.1E-17 110.4 9.6 139 5-145 8-157 (187)
14 PF10291 muHD: Muniscin C-term 99.0 1.1E-07 2.4E-12 90.5 23.5 227 173-425 3-256 (257)
15 PF03164 Mon1: Trafficking pro 95.4 0.16 3.6E-06 51.9 11.7 88 6-98 12-103 (415)
16 PF15001 AP-5_subunit_s1: AP-5 95.1 0.22 4.8E-06 44.8 10.1 79 58-136 104-183 (189)
17 KOG0997 Uncharacterized conser 92.5 1.3 2.8E-05 45.2 10.8 100 6-112 118-226 (523)
18 COG5122 TRS23 Transport protei 92.0 3.9 8.4E-05 33.4 10.9 89 4-99 2-107 (134)
19 PF04099 Sybindin: Sybindin-li 91.2 4.5 9.9E-05 34.9 11.7 94 5-99 1-116 (142)
20 PF08923 MAPKK1_Int: Mitogen-a 90.7 4.1 8.9E-05 34.0 10.5 91 5-96 17-114 (119)
21 PF13774 Longin: Regulated-SNA 90.3 1.8 3.9E-05 33.4 7.7 49 51-99 17-65 (83)
22 KOG0859 Synaptobrevin/VAMP-lik 89.7 4.4 9.5E-05 36.6 10.2 85 11-100 7-93 (217)
23 KOG0781 Signal recognition par 87.6 7.4 0.00016 40.1 11.5 113 4-119 1-116 (587)
24 PF09201 SRX: SRX; InterPro: 87.0 18 0.00039 30.8 12.0 88 4-96 1-101 (148)
25 KOG3369 Transport protein part 79.2 25 0.00054 31.1 9.8 46 52-99 125-171 (199)
26 KOG3368 Transport protein part 65.0 86 0.0019 26.6 9.8 84 3-92 1-102 (140)
27 PF13598 DUF4139: Domain of un 53.9 87 0.0019 30.5 9.3 112 249-365 194-313 (317)
28 PF08460 SH3_5: Bacterial SH3 47.7 74 0.0016 23.4 5.8 34 383-423 27-60 (65)
29 KOG0862 Synaptobrevin/VAMP-lik 47.4 2.3E+02 0.0051 26.1 10.2 49 52-100 53-101 (216)
30 PF00235 Profilin: Profilin; 40.9 2E+02 0.0043 23.5 9.0 86 5-94 16-121 (121)
31 PF14400 Transglut_i_TM: Inact 38.8 2.4E+02 0.0053 24.9 8.6 54 312-365 33-93 (165)
32 PF03504 Chlam_OMP6: Chlamydia 36.1 1.8E+02 0.0038 22.6 6.2 42 310-355 44-85 (95)
33 KOG0647 mRNA export protein (c 30.4 1.7E+02 0.0038 28.5 6.7 110 179-300 202-314 (347)
34 TIGR01451 B_ant_repeat conserv 23.0 1.9E+02 0.0041 20.1 4.3 32 291-324 11-42 (53)
35 PRK09750 hypothetical protein; 22.6 69 0.0015 23.0 1.9 14 404-417 11-24 (64)
36 PF07151 DUF1391: Protein of u 22.3 92 0.002 20.9 2.3 17 257-273 15-31 (49)
37 PF03392 OS-D: Insect pheromon 20.6 92 0.002 24.8 2.5 41 98-139 5-45 (95)
No 1
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=6.6e-103 Score=724.75 Aligned_cols=417 Identities=42% Similarity=0.755 Sum_probs=387.2
Q ss_pred ceEEEEEEcCCCCEEEEEccCCCCChhHHHHHHHHHhcccCCCCCCCCEEEeCCEEEEEEEeCcEEEEEEecCCCCHHHH
Q 014251 4 AASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAASI 83 (428)
Q Consensus 4 Mi~~i~Il~~~G~~l~~r~y~~~~~~~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~ly~v~~~~~~~n~~~~ 83 (428)
||+++||+|.+|++|+.|.||++..++..+.|.-+++... ...+|+..+++..|+|.+.++||++++|..|.|.+.+
T Consensus 1 misglfi~n~rGevlink~fr~dlkrs~~diFRv~vi~n~---d~r~PV~~igsttf~~~r~~nl~lvaitksN~Nva~v 77 (446)
T KOG0938|consen 1 MISGLFIYNLRGEVLINKTFRDDLKRSIVDIFRVQVINNL---DVRSPVLTIGSTTFHHIRSSNLWLVAITKSNANVAAV 77 (446)
T ss_pred CcceEEEEeccCcEEEehhhhhhhhhhHHHHHHHhhhhcc---ccCCCeeEecceeEEEEeeccEEEEEEecCCCchhhH
Confidence 8999999999999999999999999999999999999874 3589999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhcHHHHHhhHHHHHHHHHHHhcCCeeeecchHHHhhhccCcccccccc----c-----CCC--
Q 014251 84 LLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYRMEVT----Q-----RPP-- 152 (428)
Q Consensus 84 ~~~L~~~~~~l~~~~~~l~e~~i~~N~~~i~~lldeiid~G~p~~t~~~~l~~~i~~~~~~~~~~----~-----~~~-- 152 (428)
++||..+.+++..|||+++|+.|++||.+|||+||||+|+|+||+|++++|+..|..+++..+-. + +++
T Consensus 78 ~eFl~kl~avm~aYfgk~~Eeaiknnf~lI~ElLDemld~G~pqnte~~al~~~is~~~Vrs~g~~ls~k~s~~sq~~~~ 157 (446)
T KOG0938|consen 78 FEFLYKLDAVMNAYFGKDREEAIKNNFVLIYELLDEMLDFGIPQNTEPNALKAQISQKGVRSMGGVLSSKSSPTSQATEL 157 (446)
T ss_pred HHHHHHHHHHHHHHhcccchhhhhhceEeHHHHHHHHHhcCCCccCChhHHHhhhhhhhhhccccccCCcCCCCcccccc
Confidence 99999999999999999999999999999999999999999999999999999999887765521 1 122
Q ss_pred --CccccccccccCCCCcccceEEEEEEEeEeEEEeccCcEEEEEEEEEEEEEEEecCCCeEEEEeccchhhhc-cCC--
Q 014251 153 --MAVTNAVSWRSEGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEA-QGR-- 227 (428)
Q Consensus 153 --~~~~~~~~wR~~~~~~~~nEI~vdV~E~i~~~~~~~G~v~~~~I~G~I~~~s~LsG~P~~~l~ln~~~~~~~-~~~-- 227 (428)
++.++.++||+.|++|++||+|+||+|+++..++++|++++++|.|.|.|+|+|||||+|+++|||...+.+ ++.
T Consensus 158 ~ssqv~G~i~WRr~Gi~ykknevfldvvErvNlLmS~~GnVLrs~VsG~V~mk~~LSGmPeckfGlNDkl~~e~kq~esk 237 (446)
T KOG0938|consen 158 RSSQVTGKIGWRREGIKYKKNEVFLDVVERVNLLMSSDGNVLRSDVSGTVDMKTHLSGMPECKFGLNDKLGMESKQSESK 237 (446)
T ss_pred cccccccccccccccceeccceeEeEehheeeeEEcCCCCEEEeecccEEEEEEeccCCcccccccCcccceeecccccc
Confidence 345678999999999999999999999999999999999999999999999999999999999999987763 211
Q ss_pred ---------C-CCCceEEecccceeeeeccccccCCceEEEeCCCCceEEEEEEecCCC-CCcEEEEEEEEEccceEEEE
Q 014251 228 ---------S-TKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQV-KPLIWVEAQIERHSRSRIEI 296 (428)
Q Consensus 228 ---------~-~~~~~i~l~d~~fH~cV~~~~~~~~~~l~F~PPdG~f~Lm~Yr~~~~~-~P~~~v~~~~~~~~~~~~e~ 296 (428)
+ +....+.|+||.||+||++++|++++.|+|+||||+|+||+||+..++ +||. +.|.+++.+.+++||
T Consensus 238 s~~~n~~~~sks~~g~v~leDc~FHqCV~L~kFn~eh~IsFvPPDGe~ELMkYr~~enInlPFr-V~PiV~el~r~kie~ 316 (446)
T KOG0938|consen 238 SDFGNKNFPSKSGKGSVLLEDCTFHQCVRLDKFNSEHIISFVPPDGEFELMKYRVTENINLPFR-VTPIVTELGRTKIEY 316 (446)
T ss_pred ccccccCCCcccCCceEEeeccchheeeccccccccceEEEeCCCCceEeEeeeeccCcccceE-eeeheecccceeEEE
Confidence 1 244568999999999999999999999999999999999999999887 8886 469999988899999
Q ss_pred EEEeeccCCCcceeeeEEEEecCCCCCCCceEEecceeEEEeCCCCeEEEEeceeCCCcceEEEEEEEecCCC-ccccCC
Q 014251 297 MVKARSQFKERSTATNVEIELPVPADATNPNVRTSMGSARYAPENDALVWKIKSFPGNKEYMLRAEFSLPSIT-AEEAAP 375 (428)
Q Consensus 297 ~l~~~~~~~~~~~~~~v~v~ip~P~~~~~~~~~~~~G~~~~~~~~~~i~W~I~k~~g~~~~~l~~~~~~~~~~-~~~~~~ 375 (428)
++.+++.|++++.+.+|.++||+|+++..+.++++.|+++|.+++++++|+|+|++|.+|.+|++++++.+.. +...|
T Consensus 317 ri~iks~f~~kl~a~~v~~rIPvP~ntv~~n~~v~~Gkaky~psen~ivWki~kf~G~tE~tlsAevels~Tt~nkq~W- 395 (446)
T KOG0938|consen 317 RITIKSLFPPKLLAKDVVVRIPVPPNTVKCNISVSNGKAKYVPSENAIVWKINKFNGLTESTLSAEVELSDTTQNKQQW- 395 (446)
T ss_pred EEEEeccCCchhhhcceEEEecCCCccccceeEEecCccccCcccceEEEEecccCCcccceeEEEEEeccCccccccc-
Confidence 9999999999999999999999999999999999999999999999999999999999999999999997755 55678
Q ss_pred CCCCceEEEEEeCceeccccEEEEEEEEE-cCCCCcccceEEEEEeccEEEE
Q 014251 376 ERKAPIRVKFEIPYFTVSGIQVRYLKIIE-KSGYQALPWVRYITMAGEYELR 426 (428)
Q Consensus 376 ~~~~pi~v~F~ip~~t~SGl~V~~l~v~~-~~~~~~~k~vrY~t~sg~y~~R 426 (428)
..+||+++|++|||+.|||.|++|+|.+ +++|+..|||||+|+||+||+|
T Consensus 396 -trPPIsleFeV~MFt~SGL~VrylkV~e~~Sk~~~vkWVrYitkaGsyEiR 446 (446)
T KOG0938|consen 396 -TRPPISLEFEVPMFTNSGLVVRYLKVSEKDSKHRAVKWVRYITKAGSYEIR 446 (446)
T ss_pred -cCCCceeEEeeeeecCCceEEEEEEEecccCCCceEEEEEEecccceeeeC
Confidence 8999999999999999999999999998 5889999999999999999998
No 2
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=9.2e-91 Score=673.00 Aligned_cols=422 Identities=62% Similarity=1.044 Sum_probs=390.5
Q ss_pred eEEEEEEcCCCCEEEEEccCCCCChhHHHHHHHHHhcccCCCCCCCCEEEeCCEEEEEEEeCcEEEEEEecCCCCHHHHH
Q 014251 5 ASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAASIL 84 (428)
Q Consensus 5 i~~i~Il~~~G~~l~~r~y~~~~~~~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~ly~v~~~~~~~n~~~~~ 84 (428)
++|+||+|.+|++|++|.||++.+.+..+.|++++.... .....+|++..+|..|+|.+++++|+++++..|.+++.++
T Consensus 1 ~sa~fild~~G~~lisr~yr~dv~~s~~~~F~~~l~~~e-~~~~~~p~l~~~g~~~~~ik~s~lylv~~~~~n~~a~~v~ 79 (424)
T KOG0937|consen 1 ASAVFILDHKGEVLISRDYRGDVPMSSTEKFFRKLFEKE-EGDESPPFLVHDGSRFIHIKHSNLYLVAGTRPNVSAALVL 79 (424)
T ss_pred CceEEEEcCCCcEeEeecccccCChhhhhhHHHHHhhhc-ccCCCCCeEEeCCceEEEEeecceEEEEEeccCCCHHHHH
Confidence 479999999999999999999998899999998766543 2246789999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhhcHHHHHhhHHHHHHHHHHHhcCCeeeecchHHHhhhccCcccccccc-cCCCCcccccccccc
Q 014251 85 LFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYRMEVT-QRPPMAVTNAVSWRS 163 (428)
Q Consensus 85 ~~L~~~~~~l~~~~~~l~e~~i~~N~~~i~~lldeiid~G~p~~t~~~~l~~~i~~~~~~~~~~-~~~~~~~~~~~~wR~ 163 (428)
+||+++++++.+||+.+.|+.++.||.++||+|||++||||||.|+...|++++..+++..+.. .++|.+.+..++||+
T Consensus 80 ~~l~~~~~v~~~y~~~l~e~si~~n~vlvyElLde~mDFGypQ~t~s~iL~~yi~~~~~~l~~~~~~~p~avtnavsWrs 159 (424)
T KOG0937|consen 80 SFLYAVADVFGDYLSELEEESIRDNFVLVYELLDEVMDFGYPQTTDSEILKNYITQKANRLQDAQPRPPLAVTNAVSWRS 159 (424)
T ss_pred HHHHHHHHHHHHHhccCCccceecchHHHHHHHHHHhccCCcccchHHHHHHHhcccccceeecCCCCCcccccceeecc
Confidence 9999999999999999999999999999999999999999999999999999999997654432 256888899999999
Q ss_pred CCCCcccceEEEEEEEeEeEEEeccCcEEEEEEEEEEEEEEEecCCCeEEEEeccchhhhccCCCCCCceEEecccceee
Q 014251 164 EGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRSTKGKAIDLDDIKFHQ 243 (428)
Q Consensus 164 ~~~~~~~nEI~vdV~E~i~~~~~~~G~v~~~~I~G~I~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~i~l~d~~fH~ 243 (428)
.+++|+|||+|+||+|+++++++++|.+++++|.|+|+|||+|+|||+++|+||+...++.++..+.+..+.++|++||+
T Consensus 160 ~gi~~~KnevflDViE~Vs~l~~~~G~vl~s~i~G~I~~k~~LsGmPelrl~ln~~~~~~~~~~~~~s~~v~ledi~fh~ 239 (424)
T KOG0937|consen 160 EGIYYGKNEVFLDVIESVSLLYDSNGIVLLSEIVGTIKLKCYLSGMPELRLGLNDKVLFDKQGPRSKSKGVELEDIKFHE 239 (424)
T ss_pred cccccccceEEEEhhhhhhHhhhcCCcEEEeeeeeEEEEEEEcCCCceeeeecCcccccccccccccCcceEeeecccce
Confidence 99999999999999999999999999999999999999999999999999999999988777655556789999999999
Q ss_pred eeccccccCCceEEEeCCCCceEEEEEEecCCCCCcEEEEEEEEEccceEEEEEEEeeccCCCcceeeeEEEEecCCCCC
Q 014251 244 CVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSRIEIMVKARSQFKERSTATNVEIELPVPADA 323 (428)
Q Consensus 244 cV~~~~~~~~~~l~F~PPdG~f~Lm~Yr~~~~~~P~~~v~~~~~~~~~~~~e~~l~~~~~~~~~~~~~~v~v~ip~P~~~ 323 (428)
||++++|+.+|+|+|+||||+|+||+||++....|++++....+.++..++++.++++++|+.+..+++|.|+||+|..+
T Consensus 240 ~v~l~~fd~dr~i~FiPPdGeF~Lm~Y~ls~~vkPli~~~~~~~~~~~~ri~i~~K~~~~fk~~~~a~~v~I~iP~P~~a 319 (424)
T KOG0937|consen 240 CVRLSRFDNDRTISFIPPDGEFELMRYRLSTHVKPLIWFYQLIEEHSRSRIEVMVKLREQFKSRSSANNVEICIPVPDDA 319 (424)
T ss_pred eechhhccCCceEEecCCCCceEEEEEEecCCCCCeEEeeeeeeeccceeEEEEEechhhcCCccccceEEEEeeCCCcc
Confidence 99999999999999999999999999999999999999844444567789999999999999999999999999999999
Q ss_pred CCceEEecceeEEEeCCCCeEEEEeceeCCCcceEEEEEEEecCCCccccCCCCCCceEEEEEeCceeccccEEEEEEEE
Q 014251 324 TNPNVRTSMGSARYAPENDALVWKIKSFPGNKEYMLRAEFSLPSITAEEAAPERKAPIRVKFEIPYFTVSGIQVRYLKII 403 (428)
Q Consensus 324 ~~~~~~~~~G~~~~~~~~~~i~W~I~k~~g~~~~~l~~~~~~~~~~~~~~~~~~~~pi~v~F~ip~~t~SGl~V~~l~v~ 403 (428)
+++.+.++.|+++|.+++++++|+|++++|+.|.++++++.+++...++.-....+||+|+|+||++|.||++|+++++.
T Consensus 320 ~~~~fk~s~G~~~~~~e~~~l~W~I~~~~gg~e~~~r~~~~lp~~~~e~~~~~~~~pi~v~FeIp~~T~SgiqVrylki~ 399 (424)
T KOG0937|consen 320 SSPSFKTSLGSAKYDPEKSALRWTIKKFVGGKEYSLRARMDLPSEEHEEQCTEGLGPIKVKFEIPYFTVSGIQVRYLKII 399 (424)
T ss_pred ccceEeccCCceeeecccceEEEEeccccCCceEEEEEeecCCccccCCCCcccCCceEEEEEecccccCCeEEEEEEec
Confidence 99999999999999999999999999999999999999999998655441113789999999999999999999999999
Q ss_pred E-cCCCCcccceEEEEEeccEEEEc
Q 014251 404 E-KSGYQALPWVRYITMAGEYELRL 427 (428)
Q Consensus 404 ~-~~~~~~~k~vrY~t~sg~y~~R~ 427 (428)
+ +.+|++++||||.|+||.|++|+
T Consensus 400 ep~~~y~s~~WVRy~T~s~~Y~~r~ 424 (424)
T KOG0937|consen 400 EPKSQYQSLPWVRYNTQSGPYEIRV 424 (424)
T ss_pred ccccCCCccceEEEEccCCceEeeC
Confidence 8 68999999999999999999995
No 3
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.8e-77 Score=560.70 Aligned_cols=402 Identities=29% Similarity=0.540 Sum_probs=351.4
Q ss_pred ceEEEEEEcCCCCEEEEEccCC-CCChhHHHHHHHHHhcccCCCCCCCCEEEeCCEEEEEEEeCcEEEEEEecCCCCHHH
Q 014251 4 AASALFLLDIKGRVLIWRDYRG-DVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAAS 82 (428)
Q Consensus 4 Mi~~i~Il~~~G~~l~~r~y~~-~~~~~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~ly~v~~~~~~~n~~~ 82 (428)
||.+||++|.+|++++++.+++ ..+++.++.|+......... .+.+|++....++++-+-++++||++++..+..|++
T Consensus 1 mi~siflidtsg~l~lek~~~g~t~~rsic~~f~e~~~~~~~~-e~~ppvi~~p~hylfsv~~~~i~~~~~st~e~pPL~ 79 (418)
T KOG2740|consen 1 MILSIFLIDTSGDLLLEKHLKGSTVVRSICDYFFEDQSSDDDL-EHVPPVISTPHHYLFSVYRDLIFFCAVSTVETPPLM 79 (418)
T ss_pred CeeEEEEEcCCchhhhhHhhCCceeeeehHHHHHHhhhhcccc-ccCCceecCCceeeeeeeccCcEEEEEEeccCCChh
Confidence 8999999999999999999994 45578889998887765432 345677777777777778888999999988999999
Q ss_pred HHHHHHHHHHHHHHHHhhhcHHHHHhhHHHHHHHHHHHhcCCeeeecchHHHhhhccCccccccc----------ccCCC
Q 014251 83 ILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYRMEV----------TQRPP 152 (428)
Q Consensus 83 ~~~~L~~~~~~l~~~~~~l~e~~i~~N~~~i~~lldeiid~G~p~~t~~~~l~~~i~~~~~~~~~----------~~~~~ 152 (428)
+++||+++++++++|||+++|.+|++|++.||++||||+|+|+|..|++|.|+++|+.++..++. +...|
T Consensus 80 ~iefL~rv~dv~~eyFg~~s~~~Ik~N~~vv~ell~emiDnGfpl~tE~NiLke~i~pps~l~~~~~svTg~~n~~~~lP 159 (418)
T KOG2740|consen 80 VIEFLHRVVDVLLEYFGGLSESKIKDNVVVVYELLDEMIDNGFPLVTEPNILKELIPPPSFLSKKFNSVTGNSNVSDTLP 159 (418)
T ss_pred HHHHHHHHHHHHHHHhcccCHhHhhcceeeHHHHHHHHHHcCCCcccChhHHHhhcCChHHHHHHHhhhhccccccccCC
Confidence 99999999999999999999999999999999999999999999999999999999999988743 12456
Q ss_pred CccccccccccCCCCcccceEEEEEEEeEeEEEeccCcEEEEEEEEEEEEEEEecCCCeEEEEeccchhhhccCCCCCCc
Q 014251 153 MAVTNAVSWRSEGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRSTKGK 232 (428)
Q Consensus 153 ~~~~~~~~wR~~~~~~~~nEI~vdV~E~i~~~~~~~G~v~~~~I~G~I~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~ 232 (428)
....+.+|||+++.+|.+||.||||+|+++|+++++|..+.++|.|.|.|+|+|+|||++.|.|+++.
T Consensus 160 tg~~s~VPWR~~~~Ky~nNE~yvdvlEeidai~~k~gslv~~eI~g~vd~~~qLsgmPdltlsl~np~------------ 227 (418)
T KOG2740|consen 160 TGALSNVPWRTAGVKYTNNEAYVDVLEEIDAIVDKKGSLVFGEIQGIVDVCSQLSGMPDLTLSLNNPR------------ 227 (418)
T ss_pred CcccccccccccCcccccchhhhhhhheeheEecCCCCEEEEEEEEEEEEEEeecCCCceEEEccCcc------------
Confidence 67778899999999999999999999999999999999999999999999999999999999999864
Q ss_pred eEEecccceeeeeccccccCCceEEEeCCCCceEEEEEEecCCC---CCcEEEEEEEEEccce--EEEEEEEeeccCCCc
Q 014251 233 AIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQV---KPLIWVEAQIERHSRS--RIEIMVKARSQFKER 307 (428)
Q Consensus 233 ~i~l~d~~fH~cV~~~~~~~~~~l~F~PPdG~f~Lm~Yr~~~~~---~P~~~v~~~~~~~~~~--~~e~~l~~~~~~~~~ 307 (428)
.|+|++|||||++.+|++++.|+|+||||+|+||+||++.+. +|.. +.+++...++. ++++.+..+....+
T Consensus 228 --~L~dvsfHpcVr~krwe~~~~lsFIPPDGkFrLlsy~v~~~~~v~~pvy-v~~~i~l~~~~~~ri~~tvg~~~~~gK- 303 (418)
T KOG2740|consen 228 --LLGDVSFHPCVRYKRWESHSVLSFIPPDGKFRLLSYRVDAQNQVAIPVY-VKNSISLDSNHQGRISLTVGPKKKMGK- 303 (418)
T ss_pred --ccCCcccccceeecccccccceEEcCCCCcEEEEEEEEehhhccccceE-EeeeeccCCCceEEEEEeccccccccc-
Confidence 499999999999999999999999999999999999998653 5654 56777665443 44444443333332
Q ss_pred ceeeeEEEEecCCCCCCCceEEecceeEEEeCCCCeEEEEeceeCCCcceEEEEEEEecCCCccccCCCCCCceEEEEEe
Q 014251 308 STATNVEIELPVPADATNPNVRTSMGSARYAPENDALVWKIKSFPGNKEYMLRAEFSLPSITAEEAAPERKAPIRVKFEI 387 (428)
Q Consensus 308 ~~~~~v~v~ip~P~~~~~~~~~~~~G~~~~~~~~~~i~W~I~k~~g~~~~~l~~~~~~~~~~~~~~~~~~~~pi~v~F~i 387 (428)
..+.+.|+...|+.........++|+..++...+.+-|.++++..+.-++|++++.+.+..... . .++.++++|++
T Consensus 304 -~ie~itVt~~~pn~i~~~~k~~~~g~~~~~~~~k~l~W~~~~i~tg~lp~Lkg~~~~e~~~sk~-~--~l~t~~Lqyki 379 (418)
T KOG2740|consen 304 -TIELITVTVQDPNEIAYASKILTHGTFTNSIIMKQLTWTFGSIATGKLPVLKGTINLEPGFSKK-V--DLPTLSLQYKI 379 (418)
T ss_pred -eeEeEEEEecCccceeeeecccccceeEeecccceeEEEeecccCCcccccccccccCCCCCcc-c--cCcccceeeee
Confidence 3567889999999988888889999999999999999999999999999999999987543322 2 78999999999
Q ss_pred CceeccccEEEEEEEEEcCCCCcccceEEEEEeccEEEEc
Q 014251 388 PYFTVSGIQVRYLKIIEKSGYQALPWVRYITMAGEYELRL 427 (428)
Q Consensus 388 p~~t~SGl~V~~l~v~~~~~~~~~k~vrY~t~sg~y~~R~ 427 (428)
.+.++||++|+.|++.+ ..|++||||||.|+||.+++|+
T Consensus 380 qg~alsglkVe~Ldm~~-~~~k~yKGvKy~t~agnfqvR~ 418 (418)
T KOG2740|consen 380 QGQALSGLKVERLDMYG-EPYKPYKGVKYKTKAGNFQVRL 418 (418)
T ss_pred eeeeccceEEEeeeecC-CCCccccceEEEEeeeeEEEeC
Confidence 99999999999999997 4689999999999999999996
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=3.5e-60 Score=454.59 Aligned_cols=261 Identities=41% Similarity=0.795 Sum_probs=216.9
Q ss_pred cccccCCCCcccceEEEEEEEeEeEEEeccCcEEEEEEEEEEEEEEEecCCCeEEEEeccchhhhccCCCCCCceEEecc
Q 014251 159 VSWRSEGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRSTKGKAIDLDD 238 (428)
Q Consensus 159 ~~wR~~~~~~~~nEI~vdV~E~i~~~~~~~G~v~~~~I~G~I~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~i~l~d 238 (428)
+|||+.+++|++|||||||+|+|+|+++++|.++.++|.|+|.|+|+|+|+|+|+|+||++... ..+++.++|
T Consensus 1 ~~wR~~~~~~~~nei~vdv~E~i~~~~~~~G~~~~~~v~G~v~~~~~l~g~p~i~l~l~~~~~~-------~~~~~~l~~ 73 (262)
T PF00928_consen 1 VPWRPSGIKYKKNEIFVDVVEKISAVLDRDGNILSSEVKGSVQCKSFLSGMPEIKLTLNNPLVV-------SKNGIKLDD 73 (262)
T ss_dssp -TTS-STB--SSEEEEEEEEEEEEEEEETTSEEEEEEEEEEEEEEEE-SST-EEEEEESSSCCC-------TSSSBEESE
T ss_pred CCcccCCcccccceEEEEEEEEEEEEEccCCcEEEEEEEEEEEEEEeCCCCCeEEEEecCcccc-------ccCceeeec
Confidence 6899999999999999999999999999999999999999999999999999999999997432 124568999
Q ss_pred cceeeeeccccccCCceEEEeCCCCceEEEEEEecCCCCCcEEEEEEEEEccceEEEEEEEeeccCCCcceeeeEEEEec
Q 014251 239 IKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSRIEIMVKARSQFKERSTATNVEIELP 318 (428)
Q Consensus 239 ~~fH~cV~~~~~~~~~~l~F~PPdG~f~Lm~Yr~~~~~~P~~~v~~~~~~~~~~~~e~~l~~~~~~~~~~~~~~v~v~ip 318 (428)
++||+||++++|+++|.|+|+||||+|+||+||++....+|+.+.|++...+++++++.++++++++....+++|.|+||
T Consensus 74 ~~fH~cV~~~~~~~~~~i~f~PPdg~f~Ll~Yr~~~~~~~P~~i~~~~~~~~~~~~~v~i~~~~~~~~~~~~~~v~I~ip 153 (262)
T PF00928_consen 74 VSFHPCVDLSKFESDRVISFIPPDGEFTLLRYRVSSNSPLPFKITCWVSEKSSGRFEVTIELESNFPNKISLENVVIRIP 153 (262)
T ss_dssp EEEETTEECCCCCSHTEEEE---SEEEEEEEEEEESSS--SEEEEEEEEEETTTEEEEEEEEEE-S-TTSEEEEEEEEEE
T ss_pred eeeccccCccccccccceecCCCCceEEEEEEEccCCCCCCcEEEEEeccCCCceEEEEEEecccCCCCceeceEEEEee
Confidence 99999999999999999999999999999999998887555566899988667799999999999988888999999999
Q ss_pred CCCCCCCceEEecceeEEEeCCCCeEEEEeceeCCCcceEEEEEEEecCCCccccCCCCCCceEEEEEeCceeccccEEE
Q 014251 319 VPADATNPNVRTSMGSARYAPENDALVWKIKSFPGNKEYMLRAEFSLPSITAEEAAPERKAPIRVKFEIPYFTVSGIQVR 398 (428)
Q Consensus 319 ~P~~~~~~~~~~~~G~~~~~~~~~~i~W~I~k~~g~~~~~l~~~~~~~~~~~~~~~~~~~~pi~v~F~ip~~t~SGl~V~ 398 (428)
+|+++..+++..+.|+++|+.+++.++|+|++++++.+.+++|++++......+. ...++||+|+|++|++++||++|+
T Consensus 154 lP~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~~~~~~~~~l~~~l~~~~~~~~~~-~~~~~pi~v~F~~~~~~~Sgl~V~ 232 (262)
T PF00928_consen 154 LPPGTSSPSIESSDGSAEYDEEENALVWKIKKLPGGSESTLSGTLEFSSPSSVPS-DWSFFPISVEFTIPGYTLSGLKVR 232 (262)
T ss_dssp --TTEEEEEEEESSSEEEEETGCTEEEEEEEEEETSEEEEEEEEEEEEEECCSS--S-----EEEEEEESTSETTT-EEE
T ss_pred cCCccccceeeecCceEEEEccCCEEEEEECCccCcccccEEEEEEecCCCcccc-cccceeEEEEEEeCCcccCCCEEE
Confidence 9999889999999999999999999999999999999999999999876443332 126889999999999999999999
Q ss_pred EEEEEE-cCCCCcccceEEEEEeccEEEEc
Q 014251 399 YLKIIE-KSGYQALPWVRYITMAGEYELRL 427 (428)
Q Consensus 399 ~l~v~~-~~~~~~~k~vrY~t~sg~y~~R~ 427 (428)
+++|.+ ..+|+|+|||||+|+||+|+||+
T Consensus 233 ~l~v~~~~~~~~~~k~vky~t~s~~Y~iR~ 262 (262)
T PF00928_consen 233 SLDVVNEDENYKPYKWVKYVTKSGSYEIRT 262 (262)
T ss_dssp EEEEE-SSCGGGSEEEEEEEEEEEEEEE--
T ss_pred EEEeEecCCCCCCcccEEEEEEcCcEEEcC
Confidence 999997 36899999999999999999995
No 5
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.6e-37 Score=296.71 Aligned_cols=366 Identities=19% Similarity=0.308 Sum_probs=294.7
Q ss_pred cceEEEEEEcCCCCEEEEEccCCCCChh----HHHHHHHHHhcccCCCCCCCCEEEeCCEEEEEEEeCcEEEEEEecCCC
Q 014251 3 GAASALFLLDIKGRVLIWRDYRGDVSAI----QAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNC 78 (428)
Q Consensus 3 ~Mi~~i~Il~~~G~~l~~r~y~~~~~~~----~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~ly~v~~~~~~~ 78 (428)
||+-++.|++..|+.+++|+|+ ++++. .+.+|.+.+.. ++++.+++.+.++|||+..+.+|+|.+|+.+.
T Consensus 1 Mvvlaa~i~t~~Gk~ivsRqf~-~Msr~RIEgLl~aFpkLv~~-----~~qhT~vEt~~VRYVYqP~d~lY~vLITtk~S 74 (512)
T KOG2635|consen 1 MVVLAASINTKTGKAIVSRQFR-EMSRSRIEGLLAAFPKLVSA-----GKQHTFVETDSVRYVYQPLDNLYIVLITTKQS 74 (512)
T ss_pred CeEEEEEEeecCCceeeehHhH-hhhHHHHHHHHHHhHHhhcc-----CCCccEEecccEEEEEEecccEEEEEEecccc
Confidence 5778899999999999999999 67764 45567776663 46899999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHHHHHHhhhcHHHHHhhHHHHHHHHHHHhcCCeeeecchHHHhhhccCccccccccc---------
Q 014251 79 NAASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYRMEVTQ--------- 149 (428)
Q Consensus 79 n~~~~~~~L~~~~~~l~~~~~~l~e~~i~~N~~~i~~lldeiid~G~p~~t~~~~l~~~i~~~~~~~~~~~--------- 149 (428)
|.+..++.|+.|.+++..||..++|+.|.+|.+.+...|||++..||-...+..+++.|..+++|++++..
T Consensus 75 NIleDl~TL~Lfskvipey~~slde~eI~~~~FelifAFDEivsLGyre~v~laQikty~eMdSHEEKi~e~v~~nke~e 154 (512)
T KOG2635|consen 75 NILEDLETLRLFSKVIPEYCSSLDEKEILENAFELIFAFDEIVSLGYRENVNLAQIKTYLEMDSHEEKIHELVMRNKERE 154 (512)
T ss_pred chhhHHHHHHHHHHhchhhhhhhhHHHHHHhhhhhhhccchhhhhcccccccHHHhhhhhccccHHHHHHHHHHHhhhHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999887510
Q ss_pred ------------------------------------------------------CCC---Cc-cccccc-----------
Q 014251 150 ------------------------------------------------------RPP---MA-VTNAVS----------- 160 (428)
Q Consensus 150 ------------------------------------------------------~~~---~~-~~~~~~----------- 160 (428)
..| .+ ...+.|
T Consensus 155 a~q~mkrKaKElqr~r~ea~rrgg~~~~~~~~~~s~g~~~~s~~~~~~~~~~~~~~~~~~sa~~~~s~pak~mklG~k~~ 234 (512)
T KOG2635|consen 155 AKQEMKRKAKELQRARKEAERRGGSLNPGFDAIGSSGYSSVSTTNAINRVESIAQKPKQQSAAKASSAPAKAMKLGKKTK 234 (512)
T ss_pred HHHHHHHHHHHHHHHHHhhhccccccCCCccccccccccCCcccchhhccccccccccccccccCCCCCchhhhhccccc
Confidence 000 00 000000
Q ss_pred ------------------------cc------cCCCCcccceEEEEEEEeEeEEEeccCcEEEEEEEEEEEEEEEecCCC
Q 014251 161 ------------------------WR------SEGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMP 210 (428)
Q Consensus 161 ------------------------wR------~~~~~~~~nEI~vdV~E~i~~~~~~~G~v~~~~I~G~I~~~s~LsG~P 210 (428)
-+ +......+|.+++.+.|+|++.+++||.+.++++.|.+.++.--.--.
T Consensus 235 ~s~~~~d~Lk~ege~ia~~~s~~g~~s~aap~~~~p~v~~e~v~i~ieEkln~~~~RDGgi~s~E~qG~lsLrI~d~e~~ 314 (512)
T KOG2635|consen 235 NSDTFVDKLKGEGERIAGASSAIGSASSAAPPPTAPDVPEESVHIVIEEKLNVRLSRDGGIKSGEVQGTLSLRIKDEEYG 314 (512)
T ss_pred chhhHHHHhhccccccccccccccccccCCCCCCCCCCccceEEEEEeeeEeEEEcccCCccceeeeeeEEEEEcccccc
Confidence 00 000122345599999999999999999999999999999999877778
Q ss_pred eEEEEeccchhhhccCCCCCCceEEecccceeeeeccccccCCceEEEeCCCCceE------EEEEEecCC---CCCcEE
Q 014251 211 ECKLGLNDRVLLEAQGRSTKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFD------LMTYRLSTQ---VKPLIW 281 (428)
Q Consensus 211 ~~~l~ln~~~~~~~~~~~~~~~~i~l~d~~fH~cV~~~~~~~~~~l~F~PPdG~f~------Lm~Yr~~~~---~~P~~~ 281 (428)
.+.|.|++... .+ -++++||.+|++.|.+...|...+|+..|+ |++||.... ..|+.
T Consensus 315 ~i~lkl~n~~~----------~g---~q~ktHPNlDK~~f~s~s~iglk~~~K~FPvn~~VGvLkWR~~~~des~iPlT- 380 (512)
T KOG2635|consen 315 DIELKLANGRD----------KG---TQLKTHPNLDKKVFLSSSLIGLKRPEKPFPVNSDVGVLKWRMVDEDESEIPLT- 380 (512)
T ss_pred ceEEEEcCCCC----------cc---eeeeeCCCcchhhhccccccccccCCCCCCcCCcceEEEEeecccccccCceE-
Confidence 88999977421 22 257999999999999999999999999996 899999763 47876
Q ss_pred EEEEEEEccce---EEEEEEEeeccCCCcceeeeEEEEecCCCCCCCceEEecceeEEEeCCCCeEEEEeceeCCCcceE
Q 014251 282 VEAQIERHSRS---RIEIMVKARSQFKERSTATNVEIELPVPADATNPNVRTSMGSARYAPENDALVWKIKSFPGNKEYM 358 (428)
Q Consensus 282 v~~~~~~~~~~---~~e~~l~~~~~~~~~~~~~~v~v~ip~P~~~~~~~~~~~~G~~~~~~~~~~i~W~I~k~~g~~~~~ 358 (428)
++||.++.+.+ .+||++... ...+||.|.||+|.+. .+++....|.+.|+..++.+.|+|+.+..+..
T Consensus 381 incWPSes~~g~dV~iEYe~~~~------~eL~dV~i~iPlP~~i-apsv~~~Dge~~~~~~~~~leW~I~~Ia~N~S-- 451 (512)
T KOG2635|consen 381 INCWPSESGNGYDVNIEYEAVLE------CELNDVIITIPLPANI-APSVGECDGEYRYDERKNVLEWSIGVIAKNFS-- 451 (512)
T ss_pred EEeccccCCCCeEEEEEEeehhc------ccccceEEEeeccccc-CCccceecceEEeccccceeEEEeeeeccCCC--
Confidence 58998886543 355555322 2467999999999998 88899999999999999999999999954432
Q ss_pred EEEEEEecCCCccccCCCCCCceEEEEEeCceeccccEEEEEEEE
Q 014251 359 LRAEFSLPSITAEEAAPERKAPIRVKFEIPYFTVSGIQVRYLKII 403 (428)
Q Consensus 359 l~~~~~~~~~~~~~~~~~~~~pi~v~F~ip~~t~SGl~V~~l~v~ 403 (428)
+.++|.-.. ..+. .++|++|+|... .+++||.|.++.-.
T Consensus 452 --GslEFs~~~-~~~~--~fFPl~VsF~s~-~~ftgl~vqkVv~~ 490 (512)
T KOG2635|consen 452 --GSLEFSCPA-SDPD--GFFPLSVSFTSD-TVFTGLFVQKVVRN 490 (512)
T ss_pred --CcEEEeecC-CCCC--ceeeEEEEEEec-ccccceEEEEEEEc
Confidence 333332111 1233 899999999998 69999999976554
No 6
>KOG2677 consensus Stoned B synaptic vesicle biogenesis protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.1e-36 Score=300.56 Aligned_cols=255 Identities=27% Similarity=0.501 Sum_probs=213.3
Q ss_pred CCCcccceEEEEEEEeEeEEEeccCcEEEEEEEEEEEEEEEecCCCeEEEEeccchhhhcc---C----CCCCCceEEec
Q 014251 165 GIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQ---G----RSTKGKAIDLD 237 (428)
Q Consensus 165 ~~~~~~nEI~vdV~E~i~~~~~~~G~v~~~~I~G~I~~~s~LsG~P~~~l~ln~~~~~~~~---~----~~~~~~~i~l~ 237 (428)
...|..+||.|||.+..++.++++|.++...|..+|.|.|||+|+|+|.|+|||..+.+.. . .....+||+|.
T Consensus 581 k~nY~e~EI~v~~~Defsg~V~Keg~~~~~~v~tri~cL~FlsG~~ec~lgLND~~~kg~Eiv~rkDimp~~t~kwI~~~ 660 (922)
T KOG2677|consen 581 KSNYLEEEITVDVRDEFSGIVSKEGQILQHHVLTRIHCLSFLSGLAECRLGLNDILVKGNEIVLRKDIMPTTTTKWIKLH 660 (922)
T ss_pred ccccccceeEEEEEeccceeecccchhhhhhhhhhhhhhhhccCCceeEeecchhhhcccceeEeccccccccccceeee
Confidence 3478999999999999999999999999999999999999999999999999998764321 0 11466899999
Q ss_pred ccceeeeeccccccCCceEEEeCCCC-ceEEEEEEecCC--CCCcEEEEEEEEEccceEEEEEEEee--cc------CCC
Q 014251 238 DIKFHQCVRLARFENDRTISFIPPDG-SFDLMTYRLSTQ--VKPLIWVEAQIERHSRSRIEIMVKAR--SQ------FKE 306 (428)
Q Consensus 238 d~~fH~cV~~~~~~~~~~l~F~PPdG-~f~Lm~Yr~~~~--~~P~~~v~~~~~~~~~~~~e~~l~~~--~~------~~~ 306 (428)
+|.||.|||.+.|+++|+|.|.|||| .|+|||||+..+ .+||.+. ..+. ..|.++|++.-++ +. -..
T Consensus 661 ~~~FH~cVn~~eF~~srVI~F~PlDaCrFElMRFrt~~~~~~lpftlk-s~~~-V~Ga~VEvq~~~~mat~~qr~rd~~~ 738 (922)
T KOG2677|consen 661 ECRFHGCVNEDEFHNSRVILFNPLDACRFELMRFRTVFAEKTLPFTLK-SATS-VNGAEVEVQSWLRMATGFQRNRDPLT 738 (922)
T ss_pred eeeeecccchhhccccceEEecCcccceeeeeeeeeecCCCcCceeee-eeee-eccceeehHHHHHHHhhhhhccCccc
Confidence 99999999999999999999999999 999999999654 5898763 3333 3566788764332 22 234
Q ss_pred cceeeeEEEEecCCCCC--------------------------------CCceEEecceeEEEeCCCCeEEEEeceeCCC
Q 014251 307 RSTATNVEIELPVPADA--------------------------------TNPNVRTSMGSARYAPENDALVWKIKSFPGN 354 (428)
Q Consensus 307 ~~~~~~v~v~ip~P~~~--------------------------------~~~~~~~~~G~~~~~~~~~~i~W~I~k~~g~ 354 (428)
.+.|+||.|++|+|..| +.+.++++.|+++|++..+.+||+|+++|.+
T Consensus 739 ~vpCenI~IrfPVPs~WIk~fr~e~~~g~kSlkaK~nR~a~~gsl~~~~sepvi~vt~G~AKYEhay~siVWrI~RLPdK 818 (922)
T KOG2677|consen 739 QVPCENIMIRFPVPSEWIKNFRRESVLGEKSLKAKVNRGASFGSLSVSGSEPVIRVTLGTAKYEHAYNSIVWRINRLPDK 818 (922)
T ss_pred cCcccceeEeccCcHHHHHHHHHHhhhccchhhhhhcccccccchhhccCCceEEEeecchhhHHhhhhheeecccCCcc
Confidence 47899999999999853 1246789999999999999999999999864
Q ss_pred -----cceEEEEEEEecCCCccccCCCCCCceEEEEEeCceeccccEEEEEEEEEcCCCCcccceEEEEEeccEEEE
Q 014251 355 -----KEYMLRAEFSLPSITAEEAAPERKAPIRVKFEIPYFTVSGIQVRYLKIIEKSGYQALPWVRYITMAGEYELR 426 (428)
Q Consensus 355 -----~~~~l~~~~~~~~~~~~~~~~~~~~pi~v~F~ip~~t~SGl~V~~l~v~~~~~~~~~k~vrY~t~sg~y~~R 426 (428)
.++.|.|.++|++.++.++. ..+.+.|+|.+|..++|...||++.|+.+ -.+.|||+|.... +|++.
T Consensus 819 nsa~~hpHcl~c~lELgSd~evPs~--f~p~~~V~FsmP~t~aS~t~VRSisVE~~--~~v~K~V~y~A~Y-~yqv~ 890 (922)
T KOG2677|consen 819 NSASGHPHCLFCHLELGSDREVPSR--FAPHVNVEFSMPTTSASKTSVRSISVEDK--TDVRKWVNYSAHY-SYQVA 890 (922)
T ss_pred ccccCCCeeEEEEEeccccccCchh--hccccceeeeccccccccceeeeeecccc--ccHHHHHhhhhhe-eeeee
Confidence 47899999999998877665 67889999999999999999999999863 3589999998855 55553
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=3.8e-27 Score=204.61 Aligned_cols=135 Identities=24% Similarity=0.471 Sum_probs=116.4
Q ss_pred ceEEEEEEcCCCCEEEEEccCCCCChh---HHHHHHHHHhcccCCCCCCCCEEEeCCEEEEEEEeCcEEEEEEecCCCCH
Q 014251 4 AASALFLLDIKGRVLIWRDYRGDVSAI---QAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNA 80 (428)
Q Consensus 4 Mi~~i~Il~~~G~~l~~r~y~~~~~~~---~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~ly~v~~~~~~~n~ 80 (428)
||++++|+|++|+++++|||++..... ..+++.+.+..++ ...+|++.+++++++|++.++|||+++++.++|+
T Consensus 1 MI~~i~i~n~~G~~i~~k~y~~~~~~~~~~~~~~~~~~~~~~~---~~~~~i~~~~~~~~vy~~~~dl~~~~v~~~~eNe 77 (141)
T PF01217_consen 1 MIKAILILNSQGKRILSKYYRDVSEEERQKLFEKFIKKKSSRN---SKQSPIFEHDNYRIVYKRYSDLYFVVVGDENENE 77 (141)
T ss_dssp SEEEEEEEETTSEEEEEEESSTSTSHHHHHHHHHHHHHHHTSS---SSSTSEEEETTEEEEEEEETTEEEEEEESSTSBH
T ss_pred CEEEEEEEcCCCCEEEehhcCCccHHHHHHHHHHHHHHHHhcc---cccceeeecccceeeeEeeccEEEEEEeecccch
Confidence 999999999999999999996543332 3344444444443 3469999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcHHHHHhhHHHHHHHHHHHhcCCeeeecchHHHhhhccCc
Q 014251 81 ASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTD 141 (428)
Q Consensus 81 ~~~~~~L~~~~~~l~~~~~~l~e~~i~~N~~~i~~lldeiid~G~p~~t~~~~l~~~i~~~ 141 (428)
++++++|+++.++|+.||++++|..|++||+.+|++||||+|+|+|++||++.+.+.+.+.
T Consensus 78 l~~~e~l~~~v~~l~~~~~~v~e~~i~~N~~~v~~~LDEiid~G~i~etd~~~I~~~v~~~ 138 (141)
T PF01217_consen 78 LLLLEFLHRLVEVLDDYFGNVSEKDILENFDLVYLILDEIIDGGIILETDPNVILKRVTMQ 138 (141)
T ss_dssp HHHHHHHHHHHHHHHHHHSS-SHHHHHHTHHHHHHHHHHHEETTEES--THHHHHHHHHHC
T ss_pred HHHHHHHHHhhhhhhhhhccccHHHHHHCHHHHHHHHHHHHhCCEEEECCHHHHHHHHHHh
Confidence 9999999999999999999999999999999999999999999999999999999888753
No 8
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=99.85 E-value=9.3e-21 Score=155.70 Aligned_cols=133 Identities=14% Similarity=0.228 Sum_probs=120.0
Q ss_pred ceEEEEEEcCCCCEEEEEccCCCCC--h-hHHHHHHHHHhcccCCCCCCCCEEEeCCEEEEEEEeCcEEEEEEecCCCCH
Q 014251 4 AASALFLLDIKGRVLIWRDYRGDVS--A-IQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNA 80 (428)
Q Consensus 4 Mi~~i~Il~~~G~~l~~r~y~~~~~--~-~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~ly~v~~~~~~~n~ 80 (428)
||++++|+|++|++++.|||.+... + ..++..++.+.+++ .+.+.+++.++.+++|+++.+|||+++.+.++|+
T Consensus 1 ~i~~vli~nrqgk~RL~K~yt~~~~~e~~kli~~i~~lIs~R~---~ke~N~~e~k~~kiVYrrYA~LyF~f~Vd~~dnE 77 (152)
T COG5030 1 MIKFVLIFNRQGKPRLVKWYTPVSDPEQAKLIADIYELISARK---PKESNFIEGKNEKIVYRRYATLYFVFGVDNDDNE 77 (152)
T ss_pred CeEEEEEEcCCCceeeeEeeccCCcHHHHHHHHHHHHHHHcCC---chhcccccccCcEEEeeecCcEEEEEEEcCCCCc
Confidence 8999999999999999999975322 1 36677888888876 3588999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcHHHHHhhHHHHHHHHHHHhcCCeeeecchHHHhhhcc
Q 014251 81 ASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIK 139 (428)
Q Consensus 81 ~~~~~~L~~~~~~l~~~~~~l~e~~i~~N~~~i~~lldeiid~G~p~~t~~~~l~~~i~ 139 (428)
+.+++++|.|+++|+.||++++|.++..||..+|.+||||+-+|..++++++.+.+.+.
T Consensus 78 l~iL~lIh~FVE~lDr~FgnVCELdlIFNF~kv~~ILdE~i~gG~i~Es~~~~vl~~v~ 136 (152)
T COG5030 78 LIILELIHNFVEILDRFFGNVCELDLIFNFQKVYAILDEMILGGEIIESSKNEVLEHVY 136 (152)
T ss_pred chHHHHHHHHHHHHHHHhccceeeEeEeeHHHHHHHHHHHHhCCeeeecCHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999987665443
No 9
>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.80 E-value=1.3e-18 Score=146.23 Aligned_cols=138 Identities=16% Similarity=0.295 Sum_probs=126.7
Q ss_pred eEEEEEEcCCCCEEEEEccCCCCCh--hHHHHHHHHHhcccCCCCCCCCEEEeCCEEEEEEEeCcEEEEEEecCCCCHHH
Q 014251 5 ASALFLLDIKGRVLIWRDYRGDVSA--IQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAAS 82 (428)
Q Consensus 5 i~~i~Il~~~G~~l~~r~y~~~~~~--~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~ly~v~~~~~~~n~~~ 82 (428)
+++++|+|++|+++++|||.++.+. ....+|.+.+.+.+. .....|..++|..++|+..-||+|.++...++|+++
T Consensus 9 vk~iliLD~~G~Ri~aKYY~~~~~s~vkeqkaFEK~lF~KT~--kt~~eI~~ldg~~vvYk~~~Dl~fyv~G~~~ENEl~ 86 (175)
T KOG3343|consen 9 VKAILILDSDGKRILAKYYDDPHPSTVKEQKAFEKNLFSKTS--KTESEILLLDGNTVVYKSVIDLHFYVVGSEEENELM 86 (175)
T ss_pred hheEEEEcCCCCEeeeeecCCCcchhHHHHHHHHHHHhcccc--cccceeEEecCcEEEEEecccEEEEEecCcchhHHH
Confidence 6899999999999999999988876 355689999987764 357789999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhh-hcHHHHHhhHHHHHHHHHHHhcCCeeeecchHHHhhhccCcccc
Q 014251 83 ILLFLHRVADVFKHYFEE-LEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYR 144 (428)
Q Consensus 83 ~~~~L~~~~~~l~~~~~~-l~e~~i~~N~~~i~~lldeiid~G~p~~t~~~~l~~~i~~~~~~ 144 (428)
..+.|+.|.+.+.-.+++ ++...+.+|++.+..++|||+|+|.+++||++++...+..++..
T Consensus 87 L~svL~~l~dal~llLr~nveKr~llEN~D~i~L~~DEiiD~GvILEtdp~~ia~rv~~~~~~ 149 (175)
T KOG3343|consen 87 LMSVLTCLFDALSLLLRKNVEKRELLENLDLIFLALDEIIDGGVILETDPNQIAQRVALRPTD 149 (175)
T ss_pred HHHHHHHHHHHHHHHHHhChhHHHHHhhhccceeehhhhccCceEEecCHHHHHHHhccCCCC
Confidence 999999999999999997 89999999999999999999999999999999999999877654
No 10
>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.78 E-value=1.1e-18 Score=139.50 Aligned_cols=134 Identities=18% Similarity=0.169 Sum_probs=114.0
Q ss_pred ceEEEEEEcCCCCEEEEEccCCCCC--h-hHHHHHHHHHhcccCCCCCCCCEEEeCCEEEEEEEeCcEEEEEEecCCCCH
Q 014251 4 AASALFLLDIKGRVLIWRDYRGDVS--A-IQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNA 80 (428)
Q Consensus 4 Mi~~i~Il~~~G~~l~~r~y~~~~~--~-~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~ly~v~~~~~~~n~ 80 (428)
||..|+|.|+.|+.+++|||.+... + ...++..+.+..++. ..+..+........+++++++|||+...+...|+
T Consensus 1 mi~FILiqNr~Gk~RLak~yv~~dd~ek~~~~~~vh~lvs~Rd~--K~~~~~~~~~~~~~~~rryagLyf~~~vd~tDne 78 (143)
T KOG0935|consen 1 MIRFILIQNRAGKTRLAKWYVQFDDDEKQKLIEEVHALVTVRDA--KHTNFVEFRNFKIIYRRRYAGLYFCICVDVTDNE 78 (143)
T ss_pred CeEEEEEEccccceeheeeeeccCchHHHHHHHHHHHHHhhccc--hhhhheeeeeceEEEEEeeCCEEEEEEEecCCch
Confidence 8999999999999999999975332 2 356677777877653 2344455555556666799999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcHHHHHhhHHHHHHHHHHHhcCCeeeecchHHHhhhcc
Q 014251 81 ASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIK 139 (428)
Q Consensus 81 ~~~~~~L~~~~~~l~~~~~~l~e~~i~~N~~~i~~lldeiid~G~p~~t~~~~l~~~i~ 139 (428)
+..++.+|.|+++|+.||++++|.++..||-.||.++|||+-+|.+++|++..+.+.+.
T Consensus 79 layLe~IHlFVEvLd~fF~NVCELDlvFNFyKVy~i~DEm~l~GEi~Etsk~~vlerl~ 137 (143)
T KOG0935|consen 79 LAYLEHIHLFVEVLDEFFHNVCELDLVFNFYKVYTIVDEMFLAGEIRETSKTKVLERLL 137 (143)
T ss_pred HHHHHHHHHHHHHHHHHhccccceeeeeeeeeHHHHHHHHHHhhhhhhhhHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999988766554
No 11
>KOG0934 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.78 E-value=1.9e-19 Score=147.93 Aligned_cols=128 Identities=16% Similarity=0.228 Sum_probs=113.9
Q ss_pred ceEEEEEEcCCCCEEEEEccCCCCC--h-hHHHHHHHHHhcccCCCCCCCCEEEeCCEEEEEEEeCcEEEEEEecCCCCH
Q 014251 4 AASALFLLDIKGRVLIWRDYRGDVS--A-IQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNA 80 (428)
Q Consensus 4 Mi~~i~Il~~~G~~l~~r~y~~~~~--~-~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~ly~v~~~~~~~n~ 80 (428)
||+++++.+++|+++++|||..... + .......+.+++++ .+.|.+++..+.+.||+++++|||+|....++|+
T Consensus 1 mi~f~LlvsrQGk~rL~k~y~~~~~~er~~i~re~i~~~Lar~---pk~csfie~kd~kvVyrryasl~f~~~v~~~dNE 77 (145)
T KOG0934|consen 1 MIKFFLLVSRQGKTRLQKWYEALSIKERKKIERELIKSVLARK---PKMCSFIEYKDEKVVYRRYASLFFCVGVEDNDNE 77 (145)
T ss_pred CeEEEEEEeccCceehhHHHhhhcHHHHHHHHHHHHHHHHhCC---cccccchhccCceehhhhhhhEEEEEEEecCCch
Confidence 8999999999999999999975322 2 23445666677665 3689999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcHHHHHhhHHHHHHHHHHHhcCCeeeecchHHH
Q 014251 81 ASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKIL 134 (428)
Q Consensus 81 ~~~~~~L~~~~~~l~~~~~~l~e~~i~~N~~~i~~lldeiid~G~p~~t~~~~l 134 (428)
+.++|++|+++++|+.|||+++|.+|..||..+|.+|||.+-.|..+++..+..
T Consensus 78 L~~LE~IH~~vE~lDkYFg~VCELDiiFNfekay~ILde~~~~g~~~e~~k~~~ 131 (145)
T KOG0934|consen 78 LAILEFIHNYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEIQETSKNDV 131 (145)
T ss_pred hhHHHHHHHHHHHHHHHhccceeeEEEEehHhHHHHHHHHhcCcchHhhhcccH
Confidence 999999999999999999999999999999999999999999999998887643
No 12
>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.74 E-value=3.3e-17 Score=136.59 Aligned_cols=156 Identities=15% Similarity=0.112 Sum_probs=125.5
Q ss_pred ceEEEEEEcCCCCEEEEEccCCCCC---hhHHHHHHHHHhcccCCCCCCCCEEEe------CCEEEEEEEeCcEEEEEEe
Q 014251 4 AASALFLLDIKGRVLIWRDYRGDVS---AIQAERFFTKFIEKEGDPQSQNPVVFD------NGVTYMFIQHNNVYLMAAS 74 (428)
Q Consensus 4 Mi~~i~Il~~~G~~l~~r~y~~~~~---~~~~~~f~~~i~~~~~~~~~~~pii~~------~~~~~v~~~~~~ly~v~~~ 74 (428)
||+|++|+|.+|++++.|+|.+... +..++..+..+.++++ ..|.+.+. .+.+.+|+.+..|||+.+.
T Consensus 1 MI~AvlifNn~gkPRL~KFY~p~~~~~Qq~lir~vf~lvs~R~~---n~~nFLe~~~l~g~~d~rlIYrhYATLYFvfvv 77 (182)
T KOG0936|consen 1 MIKAVLIFNNKGKPRLVKFYTPVDEEKQQQLIREVFHLVSKRPD---NVCNFLEGNSLIGGSDNRLIYRHYATLYFVFVV 77 (182)
T ss_pred CeeEEEEecCCCCcceeeecCcCChHHHHHHHHHHHHHHHcCCc---hHhhhhccccccCCccceeehheeeeEEEEEEE
Confidence 9999999999999999999986322 2456677777777764 35666653 3579999999999999999
Q ss_pred cCCCCHHHHHHHHHHHHHHHHHHHhhhcHHHHHhhHHHHHHHHHHHhcCCeeeecchHHHhhhccCcccccccccCCCCc
Q 014251 75 RQNCNAASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYRMEVTQRPPMA 154 (428)
Q Consensus 75 ~~~~n~~~~~~~L~~~~~~l~~~~~~l~e~~i~~N~~~i~~lldeiid~G~p~~t~~~~l~~~i~~~~~~~~~~~~~~~~ 154 (428)
+..++++.++++++-|++.|+..|.+++|.++..|++.++.+|+|++.+|..++|+.+.+..-+..-+-..+.....+.+
T Consensus 78 D~sEsEL~iLDLIQvfVEtLDkCF~nVcELDliF~~~k~h~iL~EiV~GGmVlETn~neIv~av~~~nkleks~~~~~~~ 157 (182)
T KOG0936|consen 78 DSSESELGILDLIQVFVETLDKCFENVCELDLIFNWQKVHAILAEIVMGGMVLETNMNEIVAAVDEQNKLEKSEDGLIGA 157 (182)
T ss_pred cCCcchhHHHHHHHHHHHHHHHHHHhhhhhhheeeHHHHHHHHHHHHhCCeEEeccHHHHHHHHHHhchhhhccCCcccC
Confidence 99999999999999999999999999999999999999999999999999999999998777766543333322222233
Q ss_pred cccccccc
Q 014251 155 VTNAVSWR 162 (428)
Q Consensus 155 ~~~~~~wR 162 (428)
.++...|+
T Consensus 158 p~~~~~~~ 165 (182)
T KOG0936|consen 158 PTRAVFAV 165 (182)
T ss_pred chhhhhhh
Confidence 33444454
No 13
>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=99.42 E-value=9.8e-13 Score=110.45 Aligned_cols=139 Identities=16% Similarity=0.212 Sum_probs=121.3
Q ss_pred eEEEEEEcCCCCEEEEEccCCCCCh----------hHHHHHHHHHhcccCCCCCCCCEEEeCCEEEEEEEeCcEEEEEEe
Q 014251 5 ASALFLLDIKGRVLIWRDYRGDVSA----------IQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAAS 74 (428)
Q Consensus 5 i~~i~Il~~~G~~l~~r~y~~~~~~----------~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~ly~v~~~ 74 (428)
+.|++|+|++|++++.|||.+...+ .-.++|.+++..... .+...|..+++..+++.+..++.|+.+.
T Consensus 8 v~a~LilDsqGeriy~kyy~pph~~eg~~~vFnsvkkekefek~l~eKt~--k~~~~Il~f~d~lV~~k~~~dv~~yiv~ 85 (187)
T COG5541 8 VEALLILDSQGERIYRKYYQPPHRSEGHQLVFNSVKKEKEFEKKLAEKTA--KDRESILMFYDRLVMCKRLDDVLLYIVS 85 (187)
T ss_pred eeeeEEecCCccchhhhhcCCcccccccchhhcchhHHHHHHHHHHHHhh--cCccceeeEcceeeeeeeehhEEEEEec
Confidence 6899999999999999999864332 134578888876543 3577899999999999999999999999
Q ss_pred cCCCCHHHHHHHHHHHHHHHHHHHhh-hcHHHHHhhHHHHHHHHHHHhcCCeeeecchHHHhhhccCccccc
Q 014251 75 RQNCNAASILLFLHRVADVFKHYFEE-LEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYRM 145 (428)
Q Consensus 75 ~~~~n~~~~~~~L~~~~~~l~~~~~~-l~e~~i~~N~~~i~~lldeiid~G~p~~t~~~~l~~~i~~~~~~~ 145 (428)
.-++|+.++.+.+..|...|.-.++. -++..+.+|||.+..+.||.||.|.+.+|+++.+.+.++.++..+
T Consensus 86 ~meeNE~~l~q~f~~ir~Al~li~k~~~dkr~v~enYDqivl~vdEtid~Gvilet~s~~ia~rv~K~p~~E 157 (187)
T COG5541 86 PMEENEPFLGQVFDEIRAALILIVKTPTDKRNVWENYDQIVLLVDETIDEGVILETKSDEIADRVPKPPNFE 157 (187)
T ss_pred ccccccHHHHHHHHHHHHHHHHHHcCCcchhhHHhhhceEEEeeehhcccceEeecChHHHHHhCCCCCCcc
Confidence 99999999999999999999999987 566779999999999999999999999999999999999866543
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=99.03 E-value=1.1e-07 Score=90.50 Aligned_cols=227 Identities=19% Similarity=0.295 Sum_probs=120.0
Q ss_pred EEEEEEEeEeEEEeccCcEEEEEEEEEEEEEEEecC------CCeEEEEeccchhhhccCCCCCCceEEecccceeeeec
Q 014251 173 VFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSG------MPECKLGLNDRVLLEAQGRSTKGKAIDLDDIKFHQCVR 246 (428)
Q Consensus 173 I~vdV~E~i~~~~~~~G~v~~~~I~G~I~~~s~LsG------~P~~~l~ln~~~~~~~~~~~~~~~~i~l~d~~fH~cV~ 246 (428)
+-.-|.|.|||.+.. |.+.+..|.|+|.+.---.- .+.+.++|++...++ .+.-.+..=
T Consensus 3 l~asi~E~VnA~Fk~-g~~~~v~v~GEv~ls~~~~~~~~~~~~~~l~~rl~n~~~le--------------~i~pN~~~v 67 (257)
T PF10291_consen 3 LNASITETVNAYFKG-GQLSKVKVTGEVALSYPAGISSSLTSPPPLSFRLNNFSRLE--------------KIAPNPQFV 67 (257)
T ss_dssp EEEEEEEEEEEEEET-TEEEEEEEEEEEEEEEE--SSS-----SEEEEEEETGGGEE--------------EEEE-TTTE
T ss_pred eeEEEEEEEEEEEEC-CcEEEEEEEEEEEEecCCChhhcccCCCcEEEEEcCcchhc--------------eeecCHhHe
Confidence 456799999999976 78899999999998543222 345678887654322 211111100
Q ss_pred cccccCCceEEEeCCCC--ce--EEEEEEecC-----CCCCcEEEEEEEEEcc-ceEEEEEEEeec-cCCCcceeeeEEE
Q 014251 247 LARFENDRTISFIPPDG--SF--DLMTYRLST-----QVKPLIWVEAQIERHS-RSRIEIMVKARS-QFKERSTATNVEI 315 (428)
Q Consensus 247 ~~~~~~~~~l~F~PPdG--~f--~Lm~Yr~~~-----~~~P~~~v~~~~~~~~-~~~~e~~l~~~~-~~~~~~~~~~v~v 315 (428)
...-.++....|.++-= .. ..|+|++.. ...|+.+ .|..+... ...+-+.++..+ .+......+||.|
T Consensus 68 ~~~~~~~~~f~~n~~~l~~~~~~~alKYqv~~~~~~~~~~Pl~l-~~~Wk~e~~~tsl~l~Y~~Np~~~~~~~~L~nv~~ 146 (257)
T PF10291_consen 68 SSSSQSDGEFWLNMSALTSHLPKQALKYQVHSDPSNLSSVPLIL-KPVWKCEPSQTSLILDYKLNPDAFASPVPLENVVF 146 (257)
T ss_dssp --EEEETTEEEE-TTTTBT-E-EEEEEEEEES--------SEEE-EEEEEE-SSEEEEEEEEEE-TTT--E-EEEEEEEE
T ss_pred ecCCCCCCcEEEehHHhhhhhhhceEEEEEeccccccCCCCeEE-EeEEEeCCceEEEEEEEEeChhhccccceeeeEEE
Confidence 00001223344443322 22 469999976 4466654 56655433 334444445444 4444567899999
Q ss_pred EecCCCC-CCCceEEecceeEEEeCCCCeEEEEeceeC--CCcc-eEEEEEEEecCCCccccCCCCCCceEEEEEeC-ce
Q 014251 316 ELPVPAD-ATNPNVRTSMGSARYAPENDALVWKIKSFP--GNKE-YMLRAEFSLPSITAEEAAPERKAPIRVKFEIP-YF 390 (428)
Q Consensus 316 ~ip~P~~-~~~~~~~~~~G~~~~~~~~~~i~W~I~k~~--g~~~-~~l~~~~~~~~~~~~~~~~~~~~pi~v~F~ip-~~ 390 (428)
..++..+ ++++...+ .+.|..+++.+.|+++.+. +..+ ..|.|+|...... . ..++|.+.|++. +.
T Consensus 147 ~v~l~g~~~ts~~skP---~g~~~~e~~ri~Wrl~el~~~~~~~~~kL~ARf~~~~~~----~--~p~~v~vkF~~~~~~ 217 (257)
T PF10291_consen 147 SVPLDGGRATSAQSKP---QGTWNKEKNRITWRLPELSLTSEGEGGKLIARFMTSGGP----S--RPGGVEVKFEIEGGS 217 (257)
T ss_dssp EEEB-SS-EEEEEESS---S--B-SSS-EEEEE-SSEEEETT---EEEEEEEEESS----------SS-EEEEEEE---S
T ss_pred EEEcCCccccccccCC---CccccCCCcEEEEECCcccccCCCCCceEEEEEECCCCC----C--CCceEEEEEEEcCCC
Confidence 9999876 33333322 3678899999999999764 3333 7899999875521 1 568899999999 88
Q ss_pred eccccEEEEEEEEEc-----CCCCcccceEEEEEeccEEE
Q 014251 391 TVSGIQVRYLKIIEK-----SGYQALPWVRYITMAGEYEL 425 (428)
Q Consensus 391 t~SGl~V~~l~v~~~-----~~~~~~k~vrY~t~sg~y~~ 425 (428)
+.||+.|.-..=.+. .+|+.. =++-...+|.|..
T Consensus 218 ~~sg~~i~~~~~~~~~dp~~~~w~~~-~~~r~~~sGkY~~ 256 (257)
T PF10291_consen 218 TLSGLGISLVYQDDEEDPPGGGWRLV-LVKRKLVSGKYIA 256 (257)
T ss_dssp -SS----EEEEEESSS-TT----EE--EEEEEEEEEEEE-
T ss_pred cccCcEEEEeecccccCCCCCcceEE-EEEEEEeeeEEec
Confidence 899998887721111 223332 4555566899874
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=95.43 E-value=0.16 Score=51.91 Aligned_cols=88 Identities=11% Similarity=0.149 Sum_probs=58.8
Q ss_pred EEEEEEcCCCCEEEEEccCCCCC-h---hHHHHHHHHHhcccCCCCCCCCEEEeCCEEEEEEEeCcEEEEEEecCCCCHH
Q 014251 6 SALFLLDIKGRVLIWRDYRGDVS-A---IQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAA 81 (428)
Q Consensus 6 ~~i~Il~~~G~~l~~r~y~~~~~-~---~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~ly~v~~~~~~~n~~ 81 (428)
+.+||+++.||++++|+ .++.. . +++.++...+... ++.---+..++.++++..++.||+||++...+++.
T Consensus 12 kh~fIlS~AGKPIysr~-G~e~~l~~~~g~~~aiiS~~~~~----~d~l~~i~~~~~~ivfl~r~pl~lv~vS~~~e~~~ 86 (415)
T PF03164_consen 12 KHFFILSSAGKPIYSRY-GDEDKLSSLMGVIQAIISFFQSN----GDELRSIRAGDHRIVFLNRGPLILVAVSKTGESES 86 (415)
T ss_pred CeEEEECCCCceeEEec-CChHHHHHHHHHHHHHHHHHHhC----CCcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCHH
Confidence 57999999999999988 22211 1 2233333322222 22233567899999999999999999999888876
Q ss_pred HHHHHHHHHHHHHHHHH
Q 014251 82 SILLFLHRVADVFKHYF 98 (428)
Q Consensus 82 ~~~~~L~~~~~~l~~~~ 98 (428)
.+..-|+.+..-|-..+
T Consensus 87 ~l~~qL~~ly~qils~l 103 (415)
T PF03164_consen 87 QLRKQLDYLYSQILSIL 103 (415)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 66666665555544443
No 16
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=95.13 E-value=0.22 Score=44.82 Aligned_cols=79 Identities=8% Similarity=0.061 Sum_probs=70.2
Q ss_pred EEEEEEEeCcEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHhhhcH-HHHHhhHHHHHHHHHHHhcCCeeeecchHHHhh
Q 014251 58 VTYMFIQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFEELEE-ESLRDNFVVVYELLDEIMDFGFPQFTEAKILSE 136 (428)
Q Consensus 58 ~~~v~~~~~~ly~v~~~~~~~n~~~~~~~L~~~~~~l~~~~~~l~e-~~i~~N~~~i~~lldeiid~G~p~~t~~~~l~~ 136 (428)
..++.....++-|..+++..+|.+++-.||+.+...|.+.+..++. ..+...-|.|..+|+..++.|.-.-.+...++.
T Consensus 104 k~vvW~~v~~l~ftLVce~hEN~lLa~~~L~~~~~~l~~~~~~l~~~~e~l~k~d~i~aiL~~fLP~GQLLFlN~~~~k~ 183 (189)
T PF15001_consen 104 KIVVWLGVGSLCFTLVCEPHENRLLAENTLRLFIRHLLEHLKILSQPSEVLLKSDRILAILHRFLPHGQLLFLNHRFVKQ 183 (189)
T ss_pred cEEEeeccCCEEEEEEecCchhHHHHHHHHHHHHHHHHHHHHHhCcHHHhhhhHHHHHHHHHHhCCCCcEEEEcHHHHHH
Confidence 5788899999999999999999999999999999999999987544 667889999999999999999988777766554
No 17
>KOG0997 consensus Uncharacterized conserved protein Sand [Function unknown]
Probab=92.45 E-value=1.3 Score=45.22 Aligned_cols=100 Identities=20% Similarity=0.292 Sum_probs=63.2
Q ss_pred EEEEEEcCCCCEEEEEccCCCCCh---hHHHHHHHHHhcccCCCCCCCCEEEeCCEEEEEEEeCcEEEEEEecCCCCHHH
Q 014251 6 SALFLLDIKGRVLIWRDYRGDVSA---IQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAAS 82 (428)
Q Consensus 6 ~~i~Il~~~G~~l~~r~y~~~~~~---~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~ly~v~~~~~~~n~~~ 82 (428)
+.+||+.+.|+++++|+=..+.-. ++..+...-+-.. +..-.-|..+|.++++.+.+-|++||++..+..+..
T Consensus 118 khifilseaGKPiyS~~gs~e~l~stmGv~~alISf~q~~----~~~i~si~a~g~k~vfl~kspl~LvA~s~t~~Sa~q 193 (523)
T KOG0997|consen 118 KHIFILSEAGKPIYSRHGSDEALSSTMGVMQALISFFQVS----GLAITSIHAFGNKLVFLQKSPLLLVAVSRTSQSAAQ 193 (523)
T ss_pred ceEEEEecCCCceeeecCcHHHHHHHHHHHHHHHHHHhhC----CceEEEEEecCceEEEEecCcEEEEEEcccccCHHH
Confidence 469999999999999985433221 2223222222211 223346778999999999999999999987666543
Q ss_pred HHHHHHHHHHHHHHHHhhhcHHHH------HhhHHH
Q 014251 83 ILLFLHRVADVFKHYFEELEEESL------RDNFVV 112 (428)
Q Consensus 83 ~~~~L~~~~~~l~~~~~~l~e~~i------~~N~~~ 112 (428)
+++.+..+....+..|++..+ ++|||+
T Consensus 194 ---L~~qL~~ly~QIlS~LT~~ql~~if~~r~NfDL 226 (523)
T KOG0997|consen 194 ---LLQQLLLLYCQILSILTASQLQRIFNKRQNFDL 226 (523)
T ss_pred ---HHHHHHHHHHHHHHHHHHHHHHHHHhcccCchH
Confidence 444444444444445555443 468875
No 18
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=91.95 E-value=3.9 Score=33.38 Aligned_cols=89 Identities=15% Similarity=0.311 Sum_probs=53.5
Q ss_pred ceEEEEEEcCCCCEEEEEccCCCCCh----------hHHH---HHHHHHhcccCCCCCCCC--EEEeCC-EEEEEEEeCc
Q 014251 4 AASALFLLDIKGRVLIWRDYRGDVSA----------IQAE---RFFTKFIEKEGDPQSQNP--VVFDNG-VTYMFIQHNN 67 (428)
Q Consensus 4 Mi~~i~Il~~~G~~l~~r~y~~~~~~----------~~~~---~f~~~i~~~~~~~~~~~p--ii~~~~-~~~v~~~~~~ 67 (428)
.+.++||+|+.|-.+++|.|.++... +.+- ++..++..-. + ..+ ++..+. +-.+|+...+
T Consensus 2 ave~~~iINksGglifqref~~~et~lnsneyLiLastlhgV~aI~tq~~p~~---g-ssg~~~l~~~~f~m~I~qT~TG 77 (134)
T COG5122 2 AVEQFFIINKSGGLIFQREFGEGETELNSNEYLILASTLHGVSAILTQTIPLP---G-SSGRLVLYFRNFVMTIFQTTTG 77 (134)
T ss_pred ceeEEEEEecCCcEEEEEeccCCccccCcccEEEEeechhhhhhhhhhcccCC---C-CCceEEEEeccEEEEEEEecCC
Confidence 47999999999999999999654322 1111 1112221111 1 122 333443 3477888899
Q ss_pred EEEEEEe-cCCCCHHHHHHHHHHHHHHHHHHHh
Q 014251 68 VYLMAAS-RQNCNAASILLFLHRVADVFKHYFE 99 (428)
Q Consensus 68 ly~v~~~-~~~~n~~~~~~~L~~~~~~l~~~~~ 99 (428)
+-||+++ +..+|.++- |+++..+..+|.-
T Consensus 78 ~kFV~~~~k~t~na~~q---l~kiY~lYsdYV~ 107 (134)
T COG5122 78 TKFVFVAEKRTVNALFQ---LQKIYSLYSDYVT 107 (134)
T ss_pred cEEEEEecCCchhHHHH---HHHHHHHHHHHhh
Confidence 9999998 445564433 6667777666654
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=91.20 E-value=4.5 Score=34.85 Aligned_cols=94 Identities=10% Similarity=0.194 Sum_probs=53.3
Q ss_pred eEEEEEEcCCCCEEEEEccCCCC----C---hh----------HHHHHHHHHhcccCCCC--CCCC--EEEeCCEE-EEE
Q 014251 5 ASALFLLDIKGRVLIWRDYRGDV----S---AI----------QAERFFTKFIEKEGDPQ--SQNP--VVFDNGVT-YMF 62 (428)
Q Consensus 5 i~~i~Il~~~G~~l~~r~y~~~~----~---~~----------~~~~f~~~i~~~~~~~~--~~~p--ii~~~~~~-~v~ 62 (428)
|.+++|+|+.|..+++|.|.... + .+ .+.+|..++.......+ .... -++.+..+ .+|
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 67999999999999999997543 1 11 12344444443211100 1122 34556655 555
Q ss_pred EEeCcEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHh
Q 014251 63 IQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFE 99 (428)
Q Consensus 63 ~~~~~ly~v~~~~~~~n~~~~~~~L~~~~~~l~~~~~ 99 (428)
....++-||++++.+.... .-.+++.+.++.-+|.-
T Consensus 81 eT~TGlKFvl~td~~~~~~-~~~l~~~~~~lY~dyV~ 116 (142)
T PF04099_consen 81 ETPTGLKFVLITDPNVPSL-RDELLRIYYELYVDYVV 116 (142)
T ss_dssp E-TTS-EEEEEE-TTCCHC-HHHHHHHHHHHHHHHHH
T ss_pred EcCcCcEEEEEecCCCccH-HHHHHHHHHHHHHHHHh
Confidence 6678999999999888543 34467777777777753
No 20
>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=90.73 E-value=4.1 Score=34.04 Aligned_cols=91 Identities=11% Similarity=0.132 Sum_probs=61.2
Q ss_pred eEEEEEEcCCCCEEEEEccCCCCCh-----hHHHHHHHHHhcccC-CCCCCC-CEEEeCCEEEEEEEeCcEEEEEEecCC
Q 014251 5 ASALFLLDIKGRVLIWRDYRGDVSA-----IQAERFFTKFIEKEG-DPQSQN-PVVFDNGVTYMFIQHNNVYLMAASRQN 77 (428)
Q Consensus 5 i~~i~Il~~~G~~l~~r~y~~~~~~-----~~~~~f~~~i~~~~~-~~~~~~-pii~~~~~~~v~~~~~~ly~v~~~~~~ 77 (428)
+.+|+|.|++|=+++.-...+ .+. .....|-....+.++ .-+++. -+..++++.+++.....+|+..+++.+
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 LQAIVITDRDGVPIAKVSSDS-APESAMRPSLLSTFAMAIDQASKLGLGKNKSIIAYYDSYQVVQFNKLPLYITFIASSN 95 (119)
T ss_dssp EEEEEEEETTS-EEEEEE-TT-S-GGGGSHHHHCCHHHHHHHHTTSSS-SEEEEEEEESSEEEEEEEETTEEEEEEEETT
T ss_pred eEEEEEECCCCcEEEEecCCC-CcchhhhhHHHHHHHHHhhcccccCCCCceEEEEEeCCEEEEEEeCCCeEEEEEecCC
Confidence 689999999999998844333 232 122233333332221 012233 366789999999999999999999999
Q ss_pred CCHHHHHHHHHHHHHHHHH
Q 014251 78 CNAASILLFLHRVADVFKH 96 (428)
Q Consensus 78 ~n~~~~~~~L~~~~~~l~~ 96 (428)
.|.=.++.+-+.+..++.+
T Consensus 96 aN~G~il~l~~~L~~~l~~ 114 (119)
T PF08923_consen 96 ANTGLILSLEEELAPILNE 114 (119)
T ss_dssp S-HHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHhHHHHHHHHHH
Confidence 9999888888888888765
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=90.34 E-value=1.8 Score=33.38 Aligned_cols=49 Identities=6% Similarity=0.210 Sum_probs=42.6
Q ss_pred CEEEeCCEEEEEEEeCcEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHh
Q 014251 51 PVVFDNGVTYMFIQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFE 99 (428)
Q Consensus 51 pii~~~~~~~v~~~~~~ly~v~~~~~~~n~~~~~~~L~~~~~~l~~~~~ 99 (428)
-.++.++..|.+...+++.++|+|+.+-+.-.++.||+.+.+-...-++
T Consensus 17 ~s~~~~~~~fh~~~~~~i~~~citd~~~~~r~aF~fL~~i~~~F~~~~~ 65 (83)
T PF13774_consen 17 MSYESGNYVFHYLVEDGIAYLCITDKSYPKRVAFAFLEEIKQEFIQTYG 65 (83)
T ss_dssp EEEEETTEEEEEEEETTEEEEEEEETTS-HHHHHHHHHHHHHHHHHHCT
T ss_pred EEEEECCEEEEEEEcCCeEEEEEEcCCCCcchHHHHHHHHHHHHHHHcC
Confidence 4677888888888899999999999999999999999999988887776
No 22
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=89.71 E-value=4.4 Score=36.55 Aligned_cols=85 Identities=14% Similarity=0.307 Sum_probs=62.2
Q ss_pred EcCCCCEEEEEc--cCCCCChhHHHHHHHHHhcccCCCCCCCCEEEeCCEEEEEEEeCcEEEEEEecCCCCHHHHHHHHH
Q 014251 11 LDIKGRVLIWRD--YRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAASILLFLH 88 (428)
Q Consensus 11 l~~~G~~l~~r~--y~~~~~~~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~ly~v~~~~~~~n~~~~~~~L~ 88 (428)
+=.+|-++++.+ |.+.. .++.+....++... ++..--..++++.|-|...+++.++|+++.+..-...+.||+
T Consensus 7 ~VARGTvvLaeft~~~gNf-~sva~qiL~klp~~----~n~k~tYs~d~y~Fh~l~~dg~tylcvadds~gR~ipfaFLe 81 (217)
T KOG0859|consen 7 FVARGTVILAEFTEFSGNF-SSIAAQILQKLPSS----SNSKFTYSCDGYTFHYLVEDGLTYLCVADDSAGRQIPFAFLE 81 (217)
T ss_pred EEecceEEEEeeeeccCCH-HHHHHHHHHhCCCC----CCCceEEecCCeEEEEEEeCCeEEEEEEeccccccccHHHHH
Confidence 346999999977 33221 34556566655543 123446678999999999999999999998877788899999
Q ss_pred HHHHHHHHHHhh
Q 014251 89 RVADVFKHYFEE 100 (428)
Q Consensus 89 ~~~~~l~~~~~~ 100 (428)
++.+=+..-+|.
T Consensus 82 ~Ik~~F~k~YG~ 93 (217)
T KOG0859|consen 82 RIKEDFKKRYGG 93 (217)
T ss_pred HHHHHHHHHhcc
Confidence 998877666665
No 23
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=87.59 E-value=7.4 Score=40.09 Aligned_cols=113 Identities=15% Similarity=0.133 Sum_probs=73.9
Q ss_pred ceEEEEEEcCCCCEEEEEccCCCCChhHHHHHHHHHhcccCCCCCCCCEEEeCCEEEEEEEeCc--EEEEEEecCCCCHH
Q 014251 4 AASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNN--VYLMAASRQNCNAA 81 (428)
Q Consensus 4 Mi~~i~Il~~~G~~l~~r~y~~~~~~~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~--ly~v~~~~~~~n~~ 81 (428)
||+.|.|+++.|-+|..++=.++.-+..+..|++.++..... +... +..+..+.=|...|+ +.|+++-..-.+-.
T Consensus 1 Mld~faIFtkgG~vLw~~~~~~~~~~~~in~lI~~~ll~er~-~~~~--~~~~~yTlk~q~~N~~~lvfvvvfqki~~L~ 77 (587)
T KOG0781|consen 1 MLDQFAIFTKGGLVLWCYQEVGDNLKGPINALIRSVLLSERG-GVNS--FTFEAYTLKYQLDNQYSLVFVVVFQKILTLT 77 (587)
T ss_pred CcceeeeecCCcEEEEEecccchhccchHHHHHHHHHHHhhc-Cccc--CchhheeEeeeecCCccEEEEEEEeccchhh
Confidence 899999999999888875533333234566777665543221 1122 666777777777775 56667666555666
Q ss_pred HHHHHHHHHHHHHHHHHhhhcHHHHHhhHH-HHHHHHHH
Q 014251 82 SILLFLHRVADVFKHYFEELEEESLRDNFV-VVYELLDE 119 (428)
Q Consensus 82 ~~~~~L~~~~~~l~~~~~~l~e~~i~~N~~-~i~~llde 119 (428)
++-.+|....+..++-|+..+-..++.|++ +-.++|++
T Consensus 78 yv~~ll~~v~~~f~e~~~~~~~~~l~~n~~~~~~e~lk~ 116 (587)
T KOG0781|consen 78 YVDKLLNDVLNLFREKYDTQSALSLLNNTFDFQEELLKL 116 (587)
T ss_pred hHHHHHHHHHHHHHHHhccchHHHhhhhhHHHHHHHHHH
Confidence 677777777777777777666777777775 34455543
No 24
>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=87.02 E-value=18 Score=30.80 Aligned_cols=88 Identities=16% Similarity=0.218 Sum_probs=43.7
Q ss_pred ceEEEEEEcCCCCEEEEEccCC-CCChhHHHHHHHHHhcccCC---CCCCCCEEEeC-------CEEEEEEE--eCcEEE
Q 014251 4 AASALFLLDIKGRVLIWRDYRG-DVSAIQAERFFTKFIEKEGD---PQSQNPVVFDN-------GVTYMFIQ--HNNVYL 70 (428)
Q Consensus 4 Mi~~i~Il~~~G~~l~~r~y~~-~~~~~~~~~f~~~i~~~~~~---~~~~~pii~~~-------~~~~v~~~--~~~ly~ 70 (428)
||+++.|++.+|++|++..=-+ ......+.+|..++++.+.. .+...-+..+. +..+.|.. .-.|||
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 9999999999999999955222 23335678999998765421 01122333333 55555443 357999
Q ss_pred EEEecCCCCHHHHHHHHHHHHHHHHH
Q 014251 71 MAASRQNCNAASILLFLHRVADVFKH 96 (428)
Q Consensus 71 v~~~~~~~n~~~~~~~L~~~~~~l~~ 96 (428)
|++-.+ ..+++=+.-.++|+-
T Consensus 81 VvTyae-----qsleLn~EAe~~L~l 101 (148)
T PF09201_consen 81 VVTYAE-----QSLELNQEAEQTLDL 101 (148)
T ss_dssp EEEESS-------HHHHHHHHHHHHH
T ss_pred EEEecc-----ccchhhHHHHHHHHH
Confidence 988654 233444444444443
No 25
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=79.16 E-value=25 Score=31.15 Aligned_cols=46 Identities=9% Similarity=0.198 Sum_probs=33.7
Q ss_pred EEEeCC-EEEEEEEeCcEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHh
Q 014251 52 VVFDNG-VTYMFIQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFE 99 (428)
Q Consensus 52 ii~~~~-~~~v~~~~~~ly~v~~~~~~~n~~~~~~~L~~~~~~l~~~~~ 99 (428)
+++.+. .-++|+..-++=||++++.... .+=.+|+++.++..+|.=
T Consensus 125 ~LetdtF~l~~~QTlTG~KFVvis~~~~~--~aD~lLrKiYelYsDyvl 171 (199)
T KOG3369|consen 125 VLETDTFTLHIFQTLTGTKFVVIAEPGTQ--GADSLLRKIYELYSDYVL 171 (199)
T ss_pred EEEeccEEEEEEEccCCcEEEEEecCCch--hHHHHHHHHHHHHHHHhh
Confidence 334444 3588899999999999876653 445688899888888863
No 26
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=64.97 E-value=86 Score=26.55 Aligned_cols=84 Identities=11% Similarity=0.222 Sum_probs=47.2
Q ss_pred cceEEEEEEcCCCCEEEEEccCC-CC---Chh-H----------HHHHHHHHhcccCCCCCCCCEE--EeCCEEEEEEE-
Q 014251 3 GAASALFLLDIKGRVLIWRDYRG-DV---SAI-Q----------AERFFTKFIEKEGDPQSQNPVV--FDNGVTYMFIQ- 64 (428)
Q Consensus 3 ~Mi~~i~Il~~~G~~l~~r~y~~-~~---~~~-~----------~~~f~~~i~~~~~~~~~~~pii--~~~~~~~v~~~- 64 (428)
|-|.+++|+|++|..|+++.|.. .. ++. . +..|..++...+. ...+. .....+..|..
T Consensus 1 Mtiy~~yIFdR~g~Cl~y~EW~r~~~s~~~~eee~KL~yGmlFSlkS~v~Kls~~d~----k~~f~sy~Ts~YklhfyeT 76 (140)
T KOG3368|consen 1 MTIYNFYIFDRNGVCLFYREWNRTKQSGIPNEEEAKLMYGMLFSLKSFVSKLSPGDV----KDGFLSYKTSKYKLHFYET 76 (140)
T ss_pred CeEEEEEEEcCCccEEEehhcccccccCCchhHHHHHHHHHHhhHHHHHHhcCCCCc----ccCeeEEeeceeEEEEEEc
Confidence 45889999999999999977642 21 111 1 1233333332211 11222 23344433333
Q ss_pred eCcEEEEEEecCCCCHHHHHHHHHHHHH
Q 014251 65 HNNVYLMAASRQNCNAASILLFLHRVAD 92 (428)
Q Consensus 65 ~~~ly~v~~~~~~~n~~~~~~~L~~~~~ 92 (428)
-.+|.|+..|+..... +-+.||.|..
T Consensus 77 ptglk~vl~Tdpk~~~--ir~vLq~IYs 102 (140)
T KOG3368|consen 77 PTGLKFVLNTDPKAGS--IRDVLQYIYS 102 (140)
T ss_pred CCCcEEEEecCCCccc--HHHHHHHHHH
Confidence 4689999999876543 3455666655
No 27
>PF13598 DUF4139: Domain of unknown function (DUF4139)
Probab=53.90 E-value=87 Score=30.48 Aligned_cols=112 Identities=18% Similarity=0.341 Sum_probs=57.8
Q ss_pred cccCCceEEEeCCCCceEEEEEEecCCC----CCcE-EEE-EEEEEccceEEEEEEEeeccCCCcceeeeEEEEecCCCC
Q 014251 249 RFENDRTISFIPPDGSFDLMTYRLSTQV----KPLI-WVE-AQIERHSRSRIEIMVKARSQFKERSTATNVEIELPVPAD 322 (428)
Q Consensus 249 ~~~~~~~l~F~PPdG~f~Lm~Yr~~~~~----~P~~-~v~-~~~~~~~~~~~e~~l~~~~~~~~~~~~~~v~v~ip~P~~ 322 (428)
.|-.+..|.+.||+++|. |.+-.+..+ .+.. ... -.+......+.++++.++...+. .-.|.|.=++|-.
T Consensus 194 ~~vG~~~l~~~~~ge~~~-l~~G~d~~v~v~r~~~~~~~~~g~~~~~~~~~~~~~itv~N~~~~---~v~v~v~d~iPvs 269 (317)
T PF13598_consen 194 TFVGESRLPHTAPGEEFE-LSFGVDPDVRVERKLLKKEEERGFFGKSQRRTYEYTITVRNNKDE---PVTVTVEDQIPVS 269 (317)
T ss_pred EEEEeeecCCCCCCCEEE-EEcccCCCEEEEEEecceecccccccccEEEEEEEEEEEECCCCC---CEEEEEEeCCCCC
Confidence 344556788899988887 445444332 0110 000 01101111245666667654432 2357777777764
Q ss_pred CC-CceEEecc-eeEEEeCCCCeEEEEeceeCCCcceEEEEEEEe
Q 014251 323 AT-NPNVRTSM-GSARYAPENDALVWKIKSFPGNKEYMLRAEFSL 365 (428)
Q Consensus 323 ~~-~~~~~~~~-G~~~~~~~~~~i~W~I~k~~g~~~~~l~~~~~~ 365 (428)
.. ..++.... .....+...+.+.|++. ++.+.+.+++..+.+
T Consensus 270 ~~~~I~V~~~~~~~~~~~~~~g~~~W~~~-l~~g~~~~l~~~y~v 313 (317)
T PF13598_consen 270 EDEDIKVELLEPPEPNEDEKDGILEWKVT-LPPGESRTLEFSYEV 313 (317)
T ss_pred CCceEEEEEcCCCCCcccCCCCEEEEEEE-ECCCCEEEEEEEEEE
Confidence 32 22222111 12356788999999997 544444555555443
No 28
>PF08460 SH3_5: Bacterial SH3 domain; InterPro: IPR013667 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The SH3 domain has been found in a number of different bacterial proteins including glycyl-glycine endopeptidase, bacteriocin and some hypothetical proteins.; GO: 0016787 hydrolase activity; PDB: 1R77_B.
Probab=47.69 E-value=74 Score=23.39 Aligned_cols=34 Identities=32% Similarity=0.670 Sum_probs=22.9
Q ss_pred EEEEeCceeccccEEEEEEEEEcCCCCcccceEEEEEeccE
Q 014251 383 VKFEIPYFTVSGIQVRYLKIIEKSGYQALPWVRYITMAGEY 423 (428)
Q Consensus 383 v~F~ip~~t~SGl~V~~l~v~~~~~~~~~k~vrY~t~sg~y 423 (428)
+-+..+ -|-.|.+-.+....| +.|++|...+|.+
T Consensus 27 ~~~~~~----~G~~V~YD~~~~~dG---y~Wisy~~~sG~r 60 (65)
T PF08460_consen 27 VVGTYP----KGQSVNYDQVIKADG---YVWISYISYSGQR 60 (65)
T ss_dssp EEEEE-----TT-EEEEEEEEEETT---EEEEEEE-TT--E
T ss_pred eEEEEC----CCCEEEEEEEEEeCC---EEEEEEECCCCeE
Confidence 445555 788999999887666 6999999888854
No 29
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=47.41 E-value=2.3e+02 Score=26.14 Aligned_cols=49 Identities=10% Similarity=0.249 Sum_probs=43.1
Q ss_pred EEEeCCEEEEEEEeCcEEEEEEecCCCCHHHHHHHHHHHHHHHHHHHhh
Q 014251 52 VVFDNGVTYMFIQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFEE 100 (428)
Q Consensus 52 ii~~~~~~~v~~~~~~ly~v~~~~~~~n~~~~~~~L~~~~~~l~~~~~~ 100 (428)
-++.+...|.|+..+++.+.++++.+-+--+++.+|+.+.+-+..-++.
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 4567778999999999999999999999999999999999888877764
No 30
>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=40.86 E-value=2e+02 Score=23.46 Aligned_cols=86 Identities=10% Similarity=0.190 Sum_probs=49.6
Q ss_pred eEEEEEEcCCCCEEEEEc-cCCCCChhHHHHHHHHHhcccCCCCCCCCEEEeCCEEEEEEE-------------------
Q 014251 5 ASALFLLDIKGRVLIWRD-YRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQ------------------- 64 (428)
Q Consensus 5 i~~i~Il~~~G~~l~~r~-y~~~~~~~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~------------------- 64 (428)
+.+..|++.+|.+..+.- |. ..+...+..+...+..... ....-|.++|.+|...+
T Consensus 16 ~~~aaI~~~dG~vwA~s~~f~-~~~~~E~~~i~~~f~~~~~---~~~~gi~l~G~kY~~~~~d~~~i~~k~~~~G~~i~k 91 (121)
T PF00235_consen 16 ITKAAIIGSDGSVWASSPGFS-NISPEEAKAIIKAFNNPSK---FPSNGITLGGKKYIVLRADDNSIYGKKGKGGIIIVK 91 (121)
T ss_dssp ESEEEEEETTSSEEEEETTGG-GCSHHHHHHHHHHHHSSSH---HHHH-EEETTEEEEEEEEETTEEEEEETTEEEEEEE
T ss_pred EeEEEEEcCCCCEEEecCCCC-CCCHHHHHHHHHHhcCchh---cccCCeEEcCcEeEEEecCCceEEeeCCCCcEEEEE
Confidence 667788999998777643 31 1223333344443332210 11123444444444433
Q ss_pred eCcEEEEEEecCCCCHHHHHHHHHHHHHHH
Q 014251 65 HNNVYLMAASRQNCNAASILLFLHRVADVF 94 (428)
Q Consensus 65 ~~~ly~v~~~~~~~n~~~~~~~L~~~~~~l 94 (428)
.+..++++....+.+|-.+.....++++.|
T Consensus 92 t~~~ivIg~y~~~~~~~~~~~~v~~lA~yL 121 (121)
T PF00235_consen 92 TKQAIVIGMYDESIQPGNCNKAVEKLADYL 121 (121)
T ss_dssp CSSEEEEEEEETTSTHHHHHHHHHHHHHHH
T ss_pred CCCEEEEEEeCCCCCHHHHHHHHHHHHhhC
Confidence 345677888888888988888888888765
No 31
>PF14400 Transglut_i_TM: Inactive transglutaminase fused to 7 transmembrane helices
Probab=38.79 E-value=2.4e+02 Score=24.95 Aligned_cols=54 Identities=19% Similarity=0.321 Sum_probs=34.8
Q ss_pred eEEEEecCCCCCCCceE------Eecce-eEEEeCCCCeEEEEeceeCCCcceEEEEEEEe
Q 014251 312 NVEIELPVPADATNPNV------RTSMG-SARYAPENDALVWKIKSFPGNKEYMLRAEFSL 365 (428)
Q Consensus 312 ~v~v~ip~P~~~~~~~~------~~~~G-~~~~~~~~~~i~W~I~k~~g~~~~~l~~~~~~ 365 (428)
-|.|++.+|..-..-.+ +..-| +..=+..++...|+|....|.+..--+..+..
T Consensus 33 pvkvsl~lP~~~pgf~il~E~~~SpGYGls~~~~~~~RrA~WS~R~A~G~QtLYYr~~~~~ 93 (165)
T PF14400_consen 33 PVKVSLALPDTQPGFTILDENFASPGYGLSIVDDDGNRRAEWSIRRASGPQTLYYRVQLLP 93 (165)
T ss_pred CEEEEEcCCCCCCCeEEEccccccCCCCeEEEecCCCcEEEEecccCCCceEEEEEEEEEE
Confidence 57889999985333221 12233 34445568899999999999776555665543
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=36.11 E-value=1.8e+02 Score=22.59 Aligned_cols=42 Identities=24% Similarity=0.374 Sum_probs=27.4
Q ss_pred eeeEEEEecCCCCCCCceEEecceeEEEeCCCCeEEEEeceeCCCc
Q 014251 310 ATNVEIELPVPADATNPNVRTSMGSARYAPENDALVWKIKSFPGNK 355 (428)
Q Consensus 310 ~~~v~v~ip~P~~~~~~~~~~~~G~~~~~~~~~~i~W~I~k~~g~~ 355 (428)
+-||.|+-.+|-.+. +..+.-.++ -...+.++|+|+++..++
T Consensus 44 cvnVviTqqLPce~e---FV~SdPett-p~~D~kLVW~Ig~l~~G~ 85 (95)
T PF03504_consen 44 CVNVVITQQLPCEVE---FVRSDPETT-PTPDGKLVWKIGRLGQGE 85 (95)
T ss_pred eeEEEEeecCCcceE---EEecCCccc-cCCCCEEEEEeccccCCc
Confidence 568999999997543 322222222 135678999999986655
No 33
>KOG0647 consensus mRNA export protein (contains WD40 repeats) [RNA processing and modification]
Probab=30.42 E-value=1.7e+02 Score=28.53 Aligned_cols=110 Identities=15% Similarity=0.221 Sum_probs=69.6
Q ss_pred EeEeEEEeccCcEEEEEEEEEEEEEEEecCCCeEEEEeccchhhhccCCCCCCceEEecccceeeeeccccc---cCCce
Q 014251 179 ESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRSTKGKAIDLDDIKFHQCVRLARF---ENDRT 255 (428)
Q Consensus 179 E~i~~~~~~~G~v~~~~I~G~I~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~i~l~d~~fH~cV~~~~~---~~~~~ 255 (428)
-.|.+.-+++|. ....|.|.+.+..--.++|.-.+.|.-+...+. ...+-.-+.++.||| .-..| .+|.+
T Consensus 202 R~va~f~d~~~~-alGsiEGrv~iq~id~~~~~~nFtFkCHR~~~~----~~~~VYaVNsi~FhP--~hgtlvTaGsDGt 274 (347)
T KOG0647|consen 202 RCVACFQDKDGF-ALGSIEGRVAIQYIDDPNPKDNFTFKCHRSTNS----VNDDVYAVNSIAFHP--VHGTLVTAGSDGT 274 (347)
T ss_pred eEEEEEecCCce-EeeeecceEEEEecCCCCccCceeEEEeccCCC----CCCceEEecceEeec--ccceEEEecCCce
Confidence 356677788887 678899999999988999987888865532110 011223467889999 22233 35777
Q ss_pred EEEeCCCCceEEEEEEecCCCCCcEEEEEEEEEccceEEEEEEEe
Q 014251 256 ISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSRIEIMVKA 300 (428)
Q Consensus 256 l~F~PPdG~f~Lm~Yr~~~~~~P~~~v~~~~~~~~~~~~e~~l~~ 300 (428)
.+|-.-|.+-.|..|..-+ .|+. + |.|.. ++.-+-|-+.-
T Consensus 275 f~FWDkdar~kLk~s~~~~--qpIt-c-c~fn~-~G~ifaYA~gY 314 (347)
T KOG0647|consen 275 FSFWDKDARTKLKTSETHP--QPIT-C-CSFNR-NGSIFAYALGY 314 (347)
T ss_pred EEEecchhhhhhhccCcCC--Cccc-e-eEecC-CCCEEEEEeec
Confidence 7787777777777775322 3443 2 66644 34456665544
No 34
>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=22.98 E-value=1.9e+02 Score=20.12 Aligned_cols=32 Identities=22% Similarity=0.217 Sum_probs=24.2
Q ss_pred ceEEEEEEEeeccCCCcceeeeEEEEecCCCCCC
Q 014251 291 RSRIEIMVKARSQFKERSTATNVEIELPVPADAT 324 (428)
Q Consensus 291 ~~~~e~~l~~~~~~~~~~~~~~v~v~ip~P~~~~ 324 (428)
+..++|++.++..-+. .+.+|.|.=++|.+..
T Consensus 11 Gd~v~Yti~v~N~g~~--~a~~v~v~D~lP~g~~ 42 (53)
T TIGR01451 11 GDTITYTITVTNNGNV--PATNVVVTDILPSGTT 42 (53)
T ss_pred CCEEEEEEEEEECCCC--ceEeEEEEEcCCCCCE
Confidence 4478899888865433 4789999999998743
No 35
>PRK09750 hypothetical protein; Provisional
Probab=22.61 E-value=69 Score=23.05 Aligned_cols=14 Identities=43% Similarity=0.776 Sum_probs=11.4
Q ss_pred EcCCCCcccceEEE
Q 014251 404 EKSGYQALPWVRYI 417 (428)
Q Consensus 404 ~~~~~~~~k~vrY~ 417 (428)
++.|..|.+|+||.
T Consensus 11 ~KpGg~P~~W~r~s 24 (64)
T PRK09750 11 EKEGGTPTNWTRYS 24 (64)
T ss_pred ECCCCCccceeEec
Confidence 45677899999996
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=22.33 E-value=92 Score=20.88 Aligned_cols=17 Identities=47% Similarity=0.694 Sum_probs=13.6
Q ss_pred EEeCCCCceEEEEEEec
Q 014251 257 SFIPPDGSFDLMTYRLS 273 (428)
Q Consensus 257 ~F~PPdG~f~Lm~Yr~~ 273 (428)
.|---||.|+.|.|.-+
T Consensus 15 vfpn~dgtftamtytks 31 (49)
T PF07151_consen 15 VFPNQDGTFTAMTYTKS 31 (49)
T ss_pred EeeCCCCcEEEEEEeec
Confidence 45567999999999754
No 37
>PF03392 OS-D: Insect pheromone-binding family, A10/OS-D; InterPro: IPR005055 A class of small (14-20 Kd) water-soluble proteins, called odorant binding proteins (OBPs), first discovered in the insect sensillar lymph but also in the mucus of vertebrates, is postulated to mediate the solubilisation of hydrophobic odorant molecules, and thereby to facilitate their transport to the receptor neurons. The product of a gene expressed in the olfactory system of Drosophila melanogaster (Fruit fly), OS-D, shares features common to vertebrate odorant-binding proteins, but has a primary structure unlike odorant-binding proteins []. OS-D derivatives have subsequently been found in chemosensory organs of phylogenetically distinct insects, including cockroaches, phasmids and moths, suggesting that OS-D-like proteins seem to be conserved in the insect phylum.; PDB: 1KX9_A 1N8U_A 1KX8_A 1K19_A 1N8V_A 2GVS_A 2JNT_A.
Probab=20.58 E-value=92 Score=24.82 Aligned_cols=41 Identities=22% Similarity=0.407 Sum_probs=32.7
Q ss_pred HhhhcHHHHHhhHHHHHHHHHHHhcCCeeeecchHHHhhhcc
Q 014251 98 FEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIK 139 (428)
Q Consensus 98 ~~~l~e~~i~~N~~~i~~lldeiid~G~p~~t~~~~l~~~i~ 139 (428)
++.++-+.|+.|=.++-..++.++|-| |-.-+-..|+..++
T Consensus 5 yD~iDvd~iL~N~rl~~~y~~Clldkg-pCt~~~~~lK~~ip 45 (95)
T PF03392_consen 5 YDNIDVDEILKNDRLLKSYIDCLLDKG-PCTPEGKELKKVIP 45 (95)
T ss_dssp TTSSCHHHHHH-HHHHHHHHHHHTSSS-TSHHHHHHHHHHHH
T ss_pred ccccCHHHHHcCHHHHHHHHHHHhcCC-CCCHHHHHHHHHHH
Confidence 456888999999999999999999999 66556667777765
Done!