Query psy918
Match_columns 504
No_of_seqs 266 out of 1530
Neff 7.6
Searched_HMMs 46136
Date Fri Aug 16 20:58:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy918.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/918hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0938|consensus 100.0 4.8E-96 1E-100 705.1 37.8 404 99-504 1-433 (446)
2 KOG0937|consensus 100.0 1.1E-83 2.4E-88 647.8 40.5 405 100-504 1-410 (424)
3 KOG2740|consensus 100.0 9.5E-68 2.1E-72 514.4 32.0 388 99-503 1-403 (418)
4 PF00928 Adap_comp_sub: Adapto 100.0 2.8E-52 6.1E-57 414.0 26.2 246 253-504 1-248 (262)
5 KOG2635|consensus 100.0 7.6E-38 1.6E-42 311.9 31.6 368 98-495 1-491 (512)
6 KOG2677|consensus 100.0 4.3E-35 9.3E-40 301.9 8.5 271 212-496 547-872 (922)
7 PF01217 Clat_adaptor_s: Clath 99.9 1.5E-24 3.3E-29 195.3 17.4 135 99-235 1-138 (141)
8 KOG0938|consensus 99.8 1.1E-21 2.3E-26 190.7 5.0 118 1-122 26-207 (446)
9 COG5030 APS2 Clathrin adaptor 99.8 4.8E-18 1E-22 145.6 12.5 131 99-231 1-134 (152)
10 KOG0937|consensus 99.7 5.8E-18 1.3E-22 172.0 3.6 121 1-123 25-197 (424)
11 KOG3343|consensus 99.7 2.1E-16 4.5E-21 138.6 12.5 137 100-237 9-148 (175)
12 KOG0934|consensus 99.7 7E-17 1.5E-21 138.4 7.4 127 99-227 1-130 (145)
13 KOG0935|consensus 99.6 3.5E-15 7.5E-20 124.7 11.5 132 99-232 1-136 (143)
14 KOG0936|consensus 99.6 1.7E-14 3.7E-19 125.4 12.5 134 99-234 1-143 (182)
15 KOG2740|consensus 99.2 8.1E-12 1.8E-16 123.5 4.8 120 1-123 27-208 (418)
16 COG5541 RET3 Vesicle coat comp 99.2 5.6E-11 1.2E-15 104.1 8.7 137 100-237 8-155 (187)
17 PF10291 muHD: Muniscin C-term 98.8 4.6E-07 9.9E-12 89.6 20.9 204 267-491 3-227 (257)
18 PF01217 Clat_adaptor_s: Clath 95.5 0.012 2.6E-07 52.8 3.2 44 20-63 45-106 (141)
19 PF15001 AP-5_subunit_s1: AP-5 94.3 0.3 6.5E-06 45.8 9.2 80 152-231 104-184 (189)
20 PF00928 Adap_comp_sub: Adapto 93.1 0.04 8.7E-07 54.5 1.4 38 85-123 1-43 (262)
21 PF03164 Mon1: Trafficking pro 90.9 2.1 4.7E-05 45.5 11.3 88 100-192 11-103 (415)
22 PF13774 Longin: Regulated-SNA 88.4 3.9 8.5E-05 32.8 8.6 50 144-193 16-65 (83)
23 KOG0859|consensus 87.8 18 0.00039 34.1 13.3 88 103-194 4-93 (217)
24 PF08923 MAPKK1_Int: Mitogen-a 83.5 12 0.00026 32.6 9.5 91 100-191 17-115 (119)
25 COG5122 TRS23 Transport protei 70.5 68 0.0015 27.5 9.9 89 98-192 1-106 (134)
26 KOG0997|consensus 68.3 36 0.00079 36.4 9.7 71 102-175 119-192 (523)
27 KOG0781|consensus 63.1 65 0.0014 34.8 10.4 113 99-213 1-116 (587)
28 PF04099 Sybindin: Sybindin-li 61.7 1.2E+02 0.0025 27.2 10.7 92 100-192 1-115 (142)
29 PF09201 SRX: SRX; InterPro: 52.5 1.4E+02 0.003 26.7 9.0 72 99-170 1-86 (148)
30 KOG3369|consensus 41.8 2.4E+02 0.0053 26.2 9.2 45 146-192 125-170 (199)
31 KOG3368|consensus 36.0 2.5E+02 0.0054 24.9 8.0 90 98-192 1-109 (140)
32 PF00235 Profilin: Profilin; 34.1 2.9E+02 0.0063 23.4 9.2 87 100-188 16-121 (121)
33 PF13598 DUF4139: Domain of un 32.8 3.7E+02 0.0081 27.0 10.4 107 342-458 194-313 (317)
34 KOG1766|consensus 30.1 62 0.0013 26.8 3.2 43 176-218 24-68 (104)
35 KOG0862|consensus 25.9 2.3E+02 0.0051 27.2 6.7 48 146-193 53-100 (216)
36 PF03504 Chlam_OMP6: Chlamydia 23.7 4E+02 0.0087 21.6 7.2 43 402-448 43-85 (95)
No 1
>KOG0938|consensus
Probab=100.00 E-value=4.8e-96 Score=705.14 Aligned_cols=404 Identities=42% Similarity=0.749 Sum_probs=375.9
Q ss_pred heeeeEEEeCCCCeeeeeecccCcchhHHHHHHHHhhcccccCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCccHHHHH
Q psy918 99 SASALYILDVKGKVLISRNYRGDVEMGVIEKFMPLLMEKEEEGMLTPLLQTSDCTFAYIKYNNLFIVSTTKKNANIALVF 178 (504)
Q Consensus 99 ~i~~~~i~~~~G~vl~~r~y~~~~~~~~~~~f~~~v~~~~~~~~~~pv~~~~~~~~v~~~~~~ly~v~~~~~~~n~l~~~ 178 (504)
|++++||+|.+|++|++|.||++..+++.|+|+.++++.. ...+|+..++++.|+|++.++||+|++|.+|+|.++++
T Consensus 1 misglfi~n~rGevlink~fr~dlkrs~~diFRv~vi~n~--d~r~PV~~igsttf~~~r~~nl~lvaitksN~Nva~v~ 78 (446)
T KOG0938|consen 1 MISGLFIYNLRGEVLINKTFRDDLKRSIVDIFRVQVINNL--DVRSPVLTIGSTTFHHIRSSNLWLVAITKSNANVAAVF 78 (446)
T ss_pred CcceEEEEeccCcEEEehhhhhhhhhhHHHHHHHhhhhcc--ccCCCeeEecceeEEEEeeccEEEEEEecCCCchhhHH
Confidence 5899999999999999999999999999999999999873 46899999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhcccccHHHHHhhHHHHHHHHHHHHhCCcccccCHHHHHHhhhccCccccc---------CCCCC---
Q psy918 179 VFLNKIVRVFTEYFKEIEEESIRDNFVVIYELLDELIDFGYPQTTDSKILQEYITQEGHKLEI---------QPRIP--- 246 (504)
Q Consensus 179 ~~L~~i~~vl~~y~~~l~e~~i~~n~~~i~~lldEiid~G~p~~t~~~~l~~~i~~~~~~~~~---------~~~~~--- 246 (504)
+||..+..++..|||+++|+.|++||.+|||+||||+|+|+||+|++++|+.+++.+++..+- .++++
T Consensus 79 eFl~kl~avm~aYfgk~~Eeaiknnf~lI~ElLDemld~G~pqnte~~al~~~is~~~Vrs~g~~ls~k~s~~sq~~~~~ 158 (446)
T KOG0938|consen 79 EFLYKLDAVMNAYFGKDREEAIKNNFVLIYELLDEMLDFGIPQNTEPNALKAQISQKGVRSMGGVLSSKSSPTSQATELR 158 (446)
T ss_pred HHHHHHHHHHHHHhcccchhhhhhceEeHHHHHHHHHhcCCCccCChhHHHhhhhhhhhhccccccCCcCCCCccccccc
Confidence 999999999999999999999999999999999999999999999999999999987765431 11122
Q ss_pred -cccccccccccCCCccccceEEEEEEEeEEEEEccCCceEEEEEEEEEEEEEEeCCCCeEEEEecCcccccccC-C---
Q psy918 247 -MAVTNAVSWRSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVLFESTG-R--- 321 (504)
Q Consensus 247 -~~~~~~~~WR~~~~~~~~nEI~vdV~E~v~~~~~~~G~v~~~~V~G~I~~ks~LsG~P~~~l~Ln~~~~~~~~~-~--- 321 (504)
...+..++||+.|++|++||+|+||+|++|.+++++|++++++|+|.|.|+++|||||+|++||||.+.++..+ .
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 23456899999999999999999999999999999999999999999999999999999999999999886321 0
Q ss_pred ----------CCCCceeeccccccccccccCcCCCceEEEeCCCCceeEEEEEecCCCCCceEEEEEEEecccEEEEEEE
Q psy918 322 ----------GKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIERFVHSRVEYMI 391 (504)
Q Consensus 322 ----------~~~~~i~l~d~~fH~cV~~~~f~~~r~i~F~PPdG~F~Lm~Yr~~~~~~~P~~i~~~~~~~~~~~le~~l 391 (504)
.....+.||||+||+||++++|++++.|+|+||||+|+||+||++.+..+||++.|.+++.+.+++||.+
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 1234589999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EeeccCCCccccceEEEEecCCCCCCCCeEEeeeeEEEEeCCCcEEEEEeceecCCceEEEEEEEEecCCC-CCCCCCCC
Q psy918 392 KAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSVKYTPEQSAITWTIKSFPGGKEYLMRAHFGLPSVE-NEDAEGKP 470 (504)
Q Consensus 392 ~l~~~~~~~~~~~~v~I~iP~P~~~~~~~~~~s~G~~~~~~~~~~lvW~I~k~~g~~~~~l~~~~~l~s~~-~~~~~~~~ 470 (504)
++++.|+++..+.+|.++||+|.++..+++.++.|+|+|.+++++++|+|+|++|.+|.+|+|++++.+.. +...|.+|
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 99999999999999999999999999999999999999999999999999999999999999999998765 44678999
Q ss_pred CEEEEEEECCccccceEEEEEEeee-cCCCcccCC
Q psy918 471 PIQVKFEIPYFTTSGIQVRYLKIIE-KSGYQALPW 504 (504)
Q Consensus 471 pi~v~F~ip~~t~SGl~V~~l~v~~-~~~y~~~~w 504 (504)
||+++|++|||+.|||.||||+|.| +++|++.||
T Consensus 399 PIsleFeV~MFt~SGL~VrylkV~e~~Sk~~~vkW 433 (446)
T KOG0938|consen 399 PISLEFEVPMFTNSGLVVRYLKVSEKDSKHRAVKW 433 (446)
T ss_pred CceeEEeeeeecCCceEEEEEEEecccCCCceEEE
Confidence 9999999999999999999999999 478999999
No 2
>KOG0937|consensus
Probab=100.00 E-value=1.1e-83 Score=647.77 Aligned_cols=405 Identities=68% Similarity=1.079 Sum_probs=381.0
Q ss_pred eeeeEEEeCCCCeeeeeecccCcchhHHHHHHHHhhcccccCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCccHHHHHH
Q psy918 100 ASALYILDVKGKVLISRNYRGDVEMGVIEKFMPLLMEKEEEGMLTPLLQTSDCTFAYIKYNNLFIVSTTKKNANIALVFV 179 (504)
Q Consensus 100 i~~~~i~~~~G~vl~~r~y~~~~~~~~~~~f~~~v~~~~~~~~~~pv~~~~~~~~v~~~~~~ly~v~~~~~~~n~l~~~~ 179 (504)
+++++++|.+|++|++|.||++++....+.|++++......+..+|++..+|.+|+|++.++||++++++.|.+++++++
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 36889999999999999999999999999999876654333567899999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhcccccHHHHHhhHHHHHHHHHHHHhCCcccccCHHHHHHhhhccCccccc-CCCCCcccccccccccC
Q psy918 180 FLNKIVRVFTEYFKEIEEESIRDNFVVIYELLDELIDFGYPQTTDSKILQEYITQEGHKLEI-QPRIPMAVTNAVSWRSE 258 (504)
Q Consensus 180 ~L~~i~~vl~~y~~~l~e~~i~~n~~~i~~lldEiid~G~p~~t~~~~l~~~i~~~~~~~~~-~~~~~~~~~~~~~WR~~ 258 (504)
||+++++++.+||+.+.|+.+++||+++||+|||++||||||.|+.+.|++|++++++.++. ++++|.+.+++++||+.
T Consensus 81 ~l~~~~~v~~~y~~~l~e~si~~n~vlvyElLde~mDFGypQ~t~s~iL~~yi~~~~~~l~~~~~~~p~avtnavsWrs~ 160 (424)
T KOG0937|consen 81 FLYAVADVFGDYLSELEEESIRDNFVLVYELLDEVMDFGYPQTTDSEILKNYITQKANRLQDAQPRPPLAVTNAVSWRSE 160 (424)
T ss_pred HHHHHHHHHHHHhccCCccceecchHHHHHHHHHHhccCCcccchHHHHHHHhcccccceeecCCCCCcccccceeeccc
Confidence 99999999999999999999999999999999999999999999999999999999888765 34678888999999999
Q ss_pred CCccccceEEEEEEEeEEEEEccCCceEEEEEEEEEEEEEEeCCCCeEEEEecCcccccccC-CCCCCceeecccccccc
Q psy918 259 GIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVLFESTG-RGKSKSVELEDVKFHQC 337 (504)
Q Consensus 259 ~~~~~~nEI~vdV~E~v~~~~~~~G~v~~~~V~G~I~~ks~LsG~P~~~l~Ln~~~~~~~~~-~~~~~~i~l~d~~fH~c 337 (504)
|++|+|||+|+||+|+|+++++++|.++.++|.|+|.|||+|+|||+++|+||+...++..+ ++++..+.|+|++||+|
T Consensus 161 gi~~~KnevflDViE~Vs~l~~~~G~vl~s~i~G~I~~k~~LsGmPelrl~ln~~~~~~~~~~~~~s~~v~ledi~fh~~ 240 (424)
T KOG0937|consen 161 GIYYGKNEVFLDVIESVSLLYDSNGIVLLSEIVGTIKLKCYLSGMPELRLGLNDKVLFDKQGPRSKSKGVELEDIKFHEC 240 (424)
T ss_pred ccccccceEEEEhhhhhhHhhhcCCcEEEeeeeeEEEEEEEcCCCceeeeecCcccccccccccccCcceEeeeccccee
Confidence 99999999999999999999999999999999999999999999999999999999887765 66678899999999999
Q ss_pred ccccCcCCCceEEEeCCCCceeEEEEEecCCCCCceEEEEEEEecccEEEEEEEEeeccCCCccccceEEEEecCCCCCC
Q psy918 338 VRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADAD 417 (504)
Q Consensus 338 V~~~~f~~~r~i~F~PPdG~F~Lm~Yr~~~~~~~P~~i~~~~~~~~~~~le~~l~l~~~~~~~~~~~~v~I~iP~P~~~~ 417 (504)
|++++|+.+|+|+|+||||+|+||+||++...+|++++....+++++.++++.++++++|+.+..+++|+|+||+|..++
T Consensus 241 v~l~~fd~dr~i~FiPPdGeF~Lm~Y~ls~~vkPli~~~~~~~~~~~~ri~i~~K~~~~fk~~~~a~~v~I~iP~P~~a~ 320 (424)
T KOG0937|consen 241 VRLSRFDNDRTISFIPPDGEFELMRYRLSTHVKPLIWFYQLIEEHSRSRIEVMVKLREQFKSRSSANNVEICIPVPDDAS 320 (424)
T ss_pred echhhccCCceEEecCCCCceEEEEEEecCCCCCeEEeeeeeeeccceeEEEEEechhhcCCccccceEEEEeeCCCccc
Confidence 99999999999999999999999999999999999999988888888999999999999999999999999999999999
Q ss_pred CCeEEeeeeEEEEeCCCcEEEEEeceecCCceEEEEEEEEecCCCCCC--CCCCCCEEEEEEECCccccceEEEEEEeee
Q psy918 418 SPKFKTTIGSVKYTPEQSAITWTIKSFPGGKEYLMRAHFGLPSVENED--AEGKPPIQVKFEIPYFTTSGIQVRYLKIIE 495 (504)
Q Consensus 418 ~~~~~~s~G~~~~~~~~~~lvW~I~k~~g~~~~~l~~~~~l~s~~~~~--~~~~~pi~v~F~ip~~t~SGl~V~~l~v~~ 495 (504)
.+.+.++.|+++|.+++++++|+|++++|+.|..+++++.+++...++ ....+|++|+|+||++|+||++|+++++.+
T Consensus 321 ~~~fk~s~G~~~~~~e~~~l~W~I~~~~gg~e~~~r~~~~lp~~~~e~~~~~~~~pi~v~FeIp~~T~SgiqVrylki~e 400 (424)
T KOG0937|consen 321 SPSFKTSLGSAKYDPEKSALRWTIKKFVGGKEYSLRARMDLPSEEHEEQCTEGLGPIKVKFEIPYFTVSGIQVRYLKIIE 400 (424)
T ss_pred cceEeccCCceeeecccceEEEEeccccCCceEEEEEeecCCccccCCCCcccCCceEEEEEecccccCCeEEEEEEecc
Confidence 999999999999999999999999999999999999999999866545 567899999999999999999999999999
Q ss_pred c-CCCcccCC
Q psy918 496 K-SGYQALPW 504 (504)
Q Consensus 496 ~-~~y~~~~w 504 (504)
+ ++|++.+|
T Consensus 401 p~~~y~s~~W 410 (424)
T KOG0937|consen 401 PKSQYQSLPW 410 (424)
T ss_pred cccCCCccce
Confidence 4 68999999
No 3
>KOG2740|consensus
Probab=100.00 E-value=9.5e-68 Score=514.39 Aligned_cols=388 Identities=28% Similarity=0.535 Sum_probs=335.5
Q ss_pred heeeeEEEeCCCCeeeeeeccc-CcchhHHHHHHHHhhcccccCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCccHHHH
Q psy918 99 SASALYILDVKGKVLISRNYRG-DVEMGVIEKFMPLLMEKEEEGMLTPLLQTSDCTFAYIKYNNLFIVSTTKKNANIALV 177 (504)
Q Consensus 99 ~i~~~~i~~~~G~vl~~r~y~~-~~~~~~~~~f~~~v~~~~~~~~~~pv~~~~~~~~v~~~~~~ly~v~~~~~~~n~l~~ 177 (504)
|+.++|++|.+|++++.+++++ ...|++++.|++.-.........+|++..+.+.++-+-++++|||+++..+..||++
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 5899999999999999999996 556889999998776654434566777777766777888899999999999999999
Q ss_pred HHHHHHHHHHHHhhcccccHHHHHhhHHHHHHHHHHHHhCCcccccCHHHHHHhhhccCccc----------ccCCCCCc
Q psy918 178 FVFLNKIVRVFTEYFKEIEEESIRDNFVVIYELLDELIDFGYPQTTDSKILQEYITQEGHKL----------EIQPRIPM 247 (504)
Q Consensus 178 ~~~L~~i~~vl~~y~~~l~e~~i~~n~~~i~~lldEiid~G~p~~t~~~~l~~~i~~~~~~~----------~~~~~~~~ 247 (504)
++||+++++++.+|||+++|.+|++|+..||++||||+|+|+|..||+|.||++|..++... +.+...|.
T Consensus 81 iefL~rv~dv~~eyFg~~s~~~Ik~N~~vv~ell~emiDnGfpl~tE~NiLke~i~pps~l~~~~~svTg~~n~~~~lPt 160 (418)
T KOG2740|consen 81 IEFLHRVVDVLLEYFGGLSESKIKDNVVVVYELLDEMIDNGFPLVTEPNILKELIPPPSFLSKKFNSVTGNSNVSDTLPT 160 (418)
T ss_pred HHHHHHHHHHHHHHhcccCHhHhhcceeeHHHHHHHHHHcCCCcccChhHHHhhcCChHHHHHHHhhhhccccccccCCC
Confidence 99999999999999999999999999999999999999999999999999999998876532 12345677
Q ss_pred ccccccccccCCCccccceEEEEEEEeEEEEEccCCceEEEEEEEEEEEEEEeCCCCeEEEEecCcccccccCCCCCCce
Q psy918 248 AVTNAVSWRSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVLFESTGRGKSKSV 327 (504)
Q Consensus 248 ~~~~~~~WR~~~~~~~~nEI~vdV~E~v~~~~~~~G~v~~~~V~G~I~~ks~LsG~P~~~l~Ln~~~~~~~~~~~~~~~i 327 (504)
+..+.+|||+.+.||.+||.||||.|+++|+++++|..+.++|.|.+.|+|+|+|||++.|.|+++.
T Consensus 161 g~~s~VPWR~~~~Ky~nNE~yvdvlEeidai~~k~gslv~~eI~g~vd~~~qLsgmPdltlsl~np~------------- 227 (418)
T KOG2740|consen 161 GALSNVPWRTAGVKYTNNEAYVDVLEEIDAIVDKKGSLVFGEIQGIVDVCSQLSGMPDLTLSLNNPR------------- 227 (418)
T ss_pred cccccccccccCcccccchhhhhhhheeheEecCCCCEEEEEEEEEEEEEEeecCCCceEEEccCcc-------------
Confidence 7888999999999999999999999999999999999999999999999999999999999999754
Q ss_pred eeccccccccccccCcCCCceEEEeCCCCceeEEEEEecCC--CCCceEEEEEEEecc--cEEEEEEEEeeccCCCcccc
Q psy918 328 ELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTH--VKPLIWIESVIERFV--HSRVEYMIKAKSQFKRRSTA 403 (504)
Q Consensus 328 ~l~d~~fH~cV~~~~f~~~r~i~F~PPdG~F~Lm~Yr~~~~--~~~P~~i~~~~~~~~--~~~le~~l~l~~~~~~~~~~ 403 (504)
.|+|++|||||++.+|++++.|+|+||||+|+||+||+..+ .+.|..+.+.++-.+ .+++++.++.+.... ...
T Consensus 228 ~L~dvsfHpcVr~krwe~~~~lsFIPPDGkFrLlsy~v~~~~~v~~pvyv~~~i~l~~~~~~ri~~tvg~~~~~g--K~i 305 (418)
T KOG2740|consen 228 LLGDVSFHPCVRYKRWESHSVLSFIPPDGKFRLLSYRVDAQNQVAIPVYVKNSISLDSNHQGRISLTVGPKKKMG--KTI 305 (418)
T ss_pred ccCCcccccceeecccccccceEEcCCCCcEEEEEEEEehhhccccceEEeeeeccCCCceEEEEEecccccccc--cee
Confidence 69999999999999999999999999999999999999864 568888887766332 245555554443322 345
Q ss_pred ceEEEEecCCCCCCCCeEEeeeeEEEEeCCCcEEEEEeceecCCceEEEEEEEEecCCCCCCCCCCCCEEEEEEECCccc
Q psy918 404 NNVEIVIPVPADADSPKFKTTIGSVKYTPEQSAITWTIKSFPGGKEYLMRAHFGLPSVENEDAEGKPPIQVKFEIPYFTT 483 (504)
Q Consensus 404 ~~v~I~iP~P~~~~~~~~~~s~G~~~~~~~~~~lvW~I~k~~g~~~~~l~~~~~l~s~~~~~~~~~~pi~v~F~ip~~t~ 483 (504)
+.+.|+...|+........+++|+..++...+.+.|++++++.+.-+.|+|.+++... ......++.++++|++.+.++
T Consensus 306 e~itVt~~~pn~i~~~~k~~~~g~~~~~~~~k~l~W~~~~i~tg~lp~Lkg~~~~e~~-~sk~~~l~t~~Lqykiqg~al 384 (418)
T KOG2740|consen 306 ELITVTVQDPNEIAYASKILTHGTFTNSIIMKQLTWTFGSIATGKLPVLKGTINLEPG-FSKKVDLPTLSLQYKIQGQAL 384 (418)
T ss_pred EeEEEEecCccceeeeecccccceeEeecccceeEEEeecccCCcccccccccccCCC-CCccccCcccceeeeeeeeec
Confidence 6778888889998888888899999999999999999999999999999999998753 234567899999999999999
Q ss_pred cceEEEEEEeeecCCCcccC
Q psy918 484 SGIQVRYLKIIEKSGYQALP 503 (504)
Q Consensus 484 SGl~V~~l~v~~~~~y~~~~ 503 (504)
||++|..|++... .|++||
T Consensus 385 sglkVe~Ldm~~~-~~k~yK 403 (418)
T KOG2740|consen 385 SGLKVERLDMYGE-PYKPYK 403 (418)
T ss_pred cceEEEeeeecCC-CCcccc
Confidence 9999999999664 355554
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=2.8e-52 Score=414.00 Aligned_cols=246 Identities=39% Similarity=0.758 Sum_probs=206.5
Q ss_pred cccccCCCccccceEEEEEEEeEEEEEccCCceEEEEEEEEEEEEEEeCCCCeEEEEecCcccccccCCCCCCceeeccc
Q psy918 253 VSWRSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVLFESTGRGKSKSVELEDV 332 (504)
Q Consensus 253 ~~WR~~~~~~~~nEI~vdV~E~v~~~~~~~G~v~~~~V~G~I~~ks~LsG~P~~~l~Ln~~~~~~~~~~~~~~~i~l~d~ 332 (504)
+|||+.+++|++|||||||.|+|+++++++|.++.++|.|+|.|+++|+|+|+|+|+||++..+ ...++.++|+
T Consensus 1 ~~wR~~~~~~~~nei~vdv~E~i~~~~~~~G~~~~~~v~G~v~~~~~l~g~p~i~l~l~~~~~~------~~~~~~l~~~ 74 (262)
T PF00928_consen 1 VPWRPSGIKYKKNEIFVDVVEKISAVLDRDGNILSSEVKGSVQCKSFLSGMPEIKLTLNNPLVV------SKNGIKLDDV 74 (262)
T ss_dssp -TTS-STB--SSEEEEEEEEEEEEEEEETTSEEEEEEEEEEEEEEEE-SST-EEEEEESSSCCC------TSSSBEESEE
T ss_pred CCcccCCcccccceEEEEEEEEEEEEEccCCcEEEEEEEEEEEEEEeCCCCCeEEEEecCcccc------ccCceeeece
Confidence 5899999999999999999999999999999999999999999999999999999999987432 2356789999
Q ss_pred cccccccccCcCCCceEEEeCCCCceeEEEEEecCCCCCceEEEEEEEecccEEEEEEEEeeccCCCccccceEEEEecC
Q psy918 333 KFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPV 412 (504)
Q Consensus 333 ~fH~cV~~~~f~~~r~i~F~PPdG~F~Lm~Yr~~~~~~~P~~i~~~~~~~~~~~le~~l~l~~~~~~~~~~~~v~I~iP~ 412 (504)
+||+||++++|+++|.|+|+||||+|+||+||++....+||.+.+++...+..++++.++++++++....+++|.|+||+
T Consensus 75 ~fH~cV~~~~~~~~~~i~f~PPdg~f~Ll~Yr~~~~~~~P~~i~~~~~~~~~~~~~v~i~~~~~~~~~~~~~~v~I~ipl 154 (262)
T PF00928_consen 75 SFHPCVDLSKFESDRVISFIPPDGEFTLLRYRVSSNSPLPFKITCWVSEKSSGRFEVTIELESNFPNKISLENVVIRIPL 154 (262)
T ss_dssp EEETTEECCCCCSHTEEEE---SEEEEEEEEEEESSS--SEEEEEEEEEETTTEEEEEEEEEE-S-TTSEEEEEEEEEE-
T ss_pred eeccccCccccccccceecCCCCceEEEEEEEccCCCCCCcEEEEEeccCCCceEEEEEEecccCCCCceeceEEEEeec
Confidence 99999999999999999999999999999999998888999999988876678999999999998877889999999999
Q ss_pred CCCCCCCeEEeeeeEEEEeCCCcEEEEEeceecCCceEEEEEEEEecCCCCCC-CCCCCCEEEEEEECCccccceEEEEE
Q psy918 413 PADADSPKFKTTIGSVKYTPEQSAITWTIKSFPGGKEYLMRAHFGLPSVENED-AEGKPPIQVKFEIPYFTTSGIQVRYL 491 (504)
Q Consensus 413 P~~~~~~~~~~s~G~~~~~~~~~~lvW~I~k~~g~~~~~l~~~~~l~s~~~~~-~~~~~pi~v~F~ip~~t~SGl~V~~l 491 (504)
|.++..+++.++.|+++|+..++.++|+|++++++.+.+++|++++.+..... .+.++||+|+|++|++++||++|+++
T Consensus 155 P~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~pi~v~F~~~~~~~Sgl~V~~l 234 (262)
T PF00928_consen 155 PPGTSSPSIESSDGSAEYDEEENALVWKIKKLPGGSESTLSGTLEFSSPSSVPSDWSFFPISVEFTIPGYTLSGLKVRSL 234 (262)
T ss_dssp -TTEEEEEEEESSSEEEEETGCTEEEEEEEEEETSEEEEEEEEEEEEEECCSS-S-----EEEEEEESTSETTT-EEEEE
T ss_pred CCccccceeeecCceEEEEccCCEEEEEECCccCcccccEEEEEEecCCCcccccccceeEEEEEEeCCcccCCCEEEEE
Confidence 99988899999999999999999999999999999999999999997644322 23689999999999999999999999
Q ss_pred Eeeec-CCCcccCC
Q psy918 492 KIIEK-SGYQALPW 504 (504)
Q Consensus 492 ~v~~~-~~y~~~~w 504 (504)
+|.+. .+|+++||
T Consensus 235 ~v~~~~~~~~~~k~ 248 (262)
T PF00928_consen 235 DVVNEDENYKPYKW 248 (262)
T ss_dssp EEE-SSCGGGSEEE
T ss_pred EeEecCCCCCCccc
Confidence 99885 57999998
No 5
>KOG2635|consensus
Probab=100.00 E-value=7.6e-38 Score=311.87 Aligned_cols=368 Identities=21% Similarity=0.361 Sum_probs=299.1
Q ss_pred hheeeeEEEeCCCCeeeeeecccCcch----hHHHHHHHHhhcccccCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCcc
Q psy918 98 MSASALYILDVKGKVLISRNYRGDVEM----GVIEKFMPLLMEKEEEGMLTPLLQTSDCTFAYIKYNNLFIVSTTKKNAN 173 (504)
Q Consensus 98 v~i~~~~i~~~~G~vl~~r~y~~~~~~----~~~~~f~~~v~~~~~~~~~~pv~~~~~~~~v~~~~~~ly~v~~~~~~~n 173 (504)
|+.-+..+++.+|+.+++|+|+ +.+| .++.+|.+.+-. ++++.+++.+.++|||++.+++|+|.+|..+.|
T Consensus 1 Mvvlaa~i~t~~Gk~ivsRqf~-~Msr~RIEgLl~aFpkLv~~----~~qhT~vEt~~VRYVYqP~d~lY~vLITtk~SN 75 (512)
T KOG2635|consen 1 MVVLAASINTKTGKAIVSRQFR-EMSRSRIEGLLAAFPKLVSA----GKQHTFVETDSVRYVYQPLDNLYIVLITTKQSN 75 (512)
T ss_pred CeEEEEEEeecCCceeeehHhH-hhhHHHHHHHHHHhHHhhcc----CCCccEEecccEEEEEEecccEEEEEEeccccc
Confidence 4556678999999999999999 4443 468889887652 579999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhhcccccHHHHHhhHHHHHHHHHHHHhCCcccccCHHHHHHhhhccCcccc-------------
Q psy918 174 IALVFVFLNKIVRVFTEYFKEIEEESIRDNFVVIYELLDELIDFGYPQTTDSKILQEYITQEGHKLE------------- 240 (504)
Q Consensus 174 ~l~~~~~L~~i~~vl~~y~~~l~e~~i~~n~~~i~~lldEiid~G~p~~t~~~~l~~~i~~~~~~~~------------- 240 (504)
++..++.|+.|.+++.+||..++|+.|.+|.+.+...+||++..||-.+.+..++|.|..|++|+-+
T Consensus 76 IleDl~TL~Lfskvipey~~slde~eI~~~~FelifAFDEivsLGyre~v~laQikty~eMdSHEEKi~e~v~~nke~ea 155 (512)
T KOG2635|consen 76 ILEDLETLRLFSKVIPEYCSSLDEKEILENAFELIFAFDEIVSLGYRENVNLAQIKTYLEMDSHEEKIHELVMRNKEREA 155 (512)
T ss_pred hhhHHHHHHHHHHhchhhhhhhhHHHHHHhhhhhhhccchhhhhcccccccHHHhhhhhccccHHHHHHHHHHHhhhHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999997400
Q ss_pred ------------c--------C-CC-----------------------------CC----ccccccccccc---------
Q psy918 241 ------------I--------Q-PR-----------------------------IP----MAVTNAVSWRS--------- 257 (504)
Q Consensus 241 ------------~--------~-~~-----------------------------~~----~~~~~~~~WR~--------- 257 (504)
. . +. .| ....++.|-+.
T Consensus 156 ~q~mkrKaKElqr~r~ea~rrgg~~~~~~~~~~s~g~~~~s~~~~~~~~~~~~~~~~~~sa~~~~s~pak~mklG~k~~~ 235 (512)
T KOG2635|consen 156 KQEMKRKAKELQRARKEAERRGGSLNPGFDAIGSSGYSSVSTTNAINRVESIAQKPKQQSAAKASSAPAKAMKLGKKTKN 235 (512)
T ss_pred HHHHHHHHHHHHHHHHhhhccccccCCCccccccccccCCcccchhhccccccccccccccccCCCCCchhhhhcccccc
Confidence 0 0 00 00 00000111000
Q ss_pred --------------------------------CCCccccceEEEEEEEeEEEEEccCCceEEEEEEEEEEEEEEeCCCCe
Q psy918 258 --------------------------------EGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPE 305 (504)
Q Consensus 258 --------------------------------~~~~~~~nEI~vdV~E~v~~~~~~~G~v~~~~V~G~I~~ks~LsG~P~ 305 (504)
....-.++.|++.+.|+|++.++++|.+.+.++.|.+.++.-..-.-+
T Consensus 236 s~~~~d~Lk~ege~ia~~~s~~g~~s~aap~~~~p~v~~e~v~i~ieEkln~~~~RDGgi~s~E~qG~lsLrI~d~e~~~ 315 (512)
T KOG2635|consen 236 SDTFVDKLKGEGERIAGASSAIGSASSAAPPPTAPDVPEESVHIVIEEKLNVRLSRDGGIKSGEVQGTLSLRIKDEEYGD 315 (512)
T ss_pred hhhHHHHhhccccccccccccccccccCCCCCCCCCCccceEEEEEeeeEeEEEcccCCccceeeeeeEEEEEccccccc
Confidence 001122345999999999999999999999999999999999999999
Q ss_pred EEEEecCcccccccCCCCCCceeeccccccccccccCcCCCceEEEeCCCCcee------EEEEEecCC--CCCceEEEE
Q psy918 306 LRLGLNDKVLFESTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFE------LMSYRLNTH--VKPLIWIES 377 (504)
Q Consensus 306 ~~l~Ln~~~~~~~~~~~~~~~i~l~d~~fH~cV~~~~f~~~r~i~F~PPdG~F~------Lm~Yr~~~~--~~~P~~i~~ 377 (504)
+.|.|++.. ..+ -++++||++|++.|.++..|...+|+..|+ |++||.... ...|+.++|
T Consensus 316 i~lkl~n~~---------~~g---~q~ktHPNlDK~~f~s~s~iglk~~~K~FPvn~~VGvLkWR~~~~des~iPlTinc 383 (512)
T KOG2635|consen 316 IELKLANGR---------DKG---TQLKTHPNLDKKVFLSSSLIGLKRPEKPFPVNSDVGVLKWRMVDEDESEIPLTINC 383 (512)
T ss_pred eEEEEcCCC---------Ccc---eeeeeCCCcchhhhccccccccccCCCCCCcCCcceEEEEeecccccccCceEEEe
Confidence 999998632 122 358999999999999999999999999996 799998763 568999999
Q ss_pred EEEeccc---EEEEEEEEeeccCCCccccceEEEEecCCCCCCCCeEEeeeeEEEEeCCCcEEEEEeceecCCceEEEEE
Q psy918 378 VIERFVH---SRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSVKYTPEQSAITWTIKSFPGGKEYLMRA 454 (504)
Q Consensus 378 ~~~~~~~---~~le~~l~l~~~~~~~~~~~~v~I~iP~P~~~~~~~~~~s~G~~~~~~~~~~lvW~I~k~~g~~~~~l~~ 454 (504)
|.++.+. ..+||++...+ ..+||.|.||+|.++ .|......|.+.|+..++.+.|.|+.+..+. +|
T Consensus 384 WPSes~~g~dV~iEYe~~~~~------eL~dV~i~iPlP~~i-apsv~~~Dge~~~~~~~~~leW~I~~Ia~N~----SG 452 (512)
T KOG2635|consen 384 WPSESGNGYDVNIEYEAVLEC------ELNDVIITIPLPANI-APSVGECDGEYRYDERKNVLEWSIGVIAKNF----SG 452 (512)
T ss_pred ccccCCCCeEEEEEEeehhcc------cccceEEEeeccccc-CCccceecceEEeccccceeEEEeeeeccCC----CC
Confidence 9886542 36777764333 468999999999998 7888889999999999999999999994433 45
Q ss_pred EEEecCCCCCCCCCCCCEEEEEEECCccccceEEEEEEeee
Q psy918 455 HFGLPSVENEDAEGKPPIQVKFEIPYFTTSGIQVRYLKIIE 495 (504)
Q Consensus 455 ~~~l~s~~~~~~~~~~pi~v~F~ip~~t~SGl~V~~l~v~~ 495 (504)
.++|.- .....+.++|++|.|.-. .+++|+.|..+.-.+
T Consensus 453 slEFs~-~~~~~~~fFPl~VsF~s~-~~ftgl~vqkVv~~~ 491 (512)
T KOG2635|consen 453 SLEFSC-PASDPDGFFPLSVSFTSD-TVFTGLFVQKVVRND 491 (512)
T ss_pred cEEEee-cCCCCCceeeEEEEEEec-ccccceEEEEEEEcC
Confidence 555542 123578899999999997 799999999886533
No 6
>KOG2677|consensus
Probab=100.00 E-value=4.3e-35 Score=301.88 Aligned_cols=271 Identities=26% Similarity=0.455 Sum_probs=217.0
Q ss_pred HHHHhCCcccccCHHHHHHhhhccCcccccCCCCCcccccccccccCCCccccceEEEEEEEeEEEEEccCCceEEEEEE
Q psy918 212 DELIDFGYPQTTDSKILQEYITQEGHKLEIQPRIPMAVTNAVSWRSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIV 291 (504)
Q Consensus 212 dEiid~G~p~~t~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~WR~~~~~~~~nEI~vdV~E~v~~~~~~~G~v~~~~V~ 291 (504)
..|+.+| .|+..-+..||+.--..+.. .|.. |.....|..+||.|||.++.+++++++|.++...|.
T Consensus 547 eq~lKlG---stny~dfl~FittVed~Lmk---lpv~-------s~~k~nY~e~EI~v~~~Defsg~V~Keg~~~~~~v~ 613 (922)
T KOG2677|consen 547 EQVLKLG---STNYDDFLSFITTVEDRLMK---LPVL-------SMDKSNYLEEEITVDVRDEFSGIVSKEGQILQHHVL 613 (922)
T ss_pred hhhhhcc---CCcHHHHHHHHHHHHHHHhc---Cccc-------cccccccccceeEEEEEeccceeecccchhhhhhhh
Confidence 4455677 46666666666542211110 1111 112237999999999999999999999999999999
Q ss_pred EEEEEEEEeCCCCeEEEEecCcccccccC--------CCCCCceeeccccccccccccCcCCCceEEEeCCCC-ceeEEE
Q psy918 292 GAIKMRVYLSGMPELRLGLNDKVLFESTG--------RGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDG-EFELMS 362 (504)
Q Consensus 292 G~I~~ks~LsG~P~~~l~Ln~~~~~~~~~--------~~~~~~i~l~d~~fH~cV~~~~f~~~r~i~F~PPdG-~F~Lm~ 362 (504)
.+|.|.|||+|.|+|.|+|||..+.+..- .....||+|.+|.||.||+.+.|+++|+|.|.|||| .|+|||
T Consensus 614 tri~cL~FlsG~~ec~lgLND~~~kg~Eiv~rkDimp~~t~kwI~~~~~~FH~cVn~~eF~~srVI~F~PlDaCrFElMR 693 (922)
T KOG2677|consen 614 TRIHCLSFLSGLAECRLGLNDILVKGNEIVLRKDIMPTTTTKWIKLHECRFHGCVNEDEFHNSRVILFNPLDACRFELMR 693 (922)
T ss_pred hhhhhhhhccCCceeEeecchhhhcccceeEeccccccccccceeeeeeeeecccchhhccccceEEecCcccceeeeee
Confidence 99999999999999999999987643321 124689999999999999999999999999999999 899999
Q ss_pred EEecCC-CCCceEEEEEEEecccEEEEEEE--EeeccCC------CccccceEEEEecCCCCC-----------------
Q psy918 363 YRLNTH-VKPLIWIESVIERFVHSRVEYMI--KAKSQFK------RRSTANNVEIVIPVPADA----------------- 416 (504)
Q Consensus 363 Yr~~~~-~~~P~~i~~~~~~~~~~~le~~l--~l~~~~~------~~~~~~~v~I~iP~P~~~----------------- 416 (504)
||+..+ ...||.++..+.-.| .++|++. ++.+.|. ....|+||.|++|+|..|
T Consensus 694 Frt~~~~~~lpftlks~~~V~G-a~VEvq~~~~mat~~qr~rd~~~~vpCenI~IrfPVPs~WIk~fr~e~~~g~kSlka 772 (922)
T KOG2677|consen 694 FRTVFAEKTLPFTLKSATSVNG-AEVEVQSWLRMATGFQRNRDPLTQVPCENIMIRFPVPSEWIKNFRRESVLGEKSLKA 772 (922)
T ss_pred eeeecCCCcCceeeeeeeeecc-ceeehHHHHHHHhhhhhccCccccCcccceeEeccCcHHHHHHHHHHhhhccchhhh
Confidence 999865 468999988766443 4566653 2222222 346899999999999853
Q ss_pred ---------------CCCeEEeeeeEEEEeCCCcEEEEEeceecCCc-----eEEEEEEEEecCCCCCCCCCCCCEEEEE
Q psy918 417 ---------------DSPKFKTTIGSVKYTPEQSAITWTIKSFPGGK-----EYLMRAHFGLPSVENEDAEGKPPIQVKF 476 (504)
Q Consensus 417 ---------------~~~~~~~s~G~~~~~~~~~~lvW~I~k~~g~~-----~~~l~~~~~l~s~~~~~~~~~~pi~v~F 476 (504)
+.+.++++.|+|+|++..+.+||+|+++|.++ .+.|.|.++|++....+.+..+.+.|+|
T Consensus 773 K~nR~a~~gsl~~~~sepvi~vt~G~AKYEhay~siVWrI~RLPdKnsa~~hpHcl~c~lELgSd~evPs~f~p~~~V~F 852 (922)
T KOG2677|consen 773 KVNRGASFGSLSVSGSEPVIRVTLGTAKYEHAYNSIVWRINRLPDKNSASGHPHCLFCHLELGSDREVPSRFAPHVNVEF 852 (922)
T ss_pred hhcccccccchhhccCCceEEEeecchhhHHhhhhheeecccCCccccccCCCeeEEEEEeccccccCchhhccccceee
Confidence 23568899999999999999999999999755 6789999999998776777789999999
Q ss_pred EECCccccceEEEEEEeeec
Q psy918 477 EIPYFTTSGIQVRYLKIIEK 496 (504)
Q Consensus 477 ~ip~~t~SGl~V~~l~v~~~ 496 (504)
.+|..++|...||++.|+.+
T Consensus 853 smP~t~aS~t~VRSisVE~~ 872 (922)
T KOG2677|consen 853 SMPTTSASKTSVRSISVEDK 872 (922)
T ss_pred eccccccccceeeeeecccc
Confidence 99999999999999999764
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=99.93 E-value=1.5e-24 Score=195.31 Aligned_cols=135 Identities=30% Similarity=0.571 Sum_probs=117.0
Q ss_pred heeeeEEEeCCCCeeeeeecccCcchh---HHHHHHHHhhcccccCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCccHH
Q psy918 99 SASALYILDVKGKVLISRNYRGDVEMG---VIEKFMPLLMEKEEEGMLTPLLQTSDCTFAYIKYNNLFIVSTTKKNANIA 175 (504)
Q Consensus 99 ~i~~~~i~~~~G~vl~~r~y~~~~~~~---~~~~f~~~v~~~~~~~~~~pv~~~~~~~~v~~~~~~ly~v~~~~~~~n~l 175 (504)
|+++++|+|.+|+++++|+|++...+. ..+.+.+.+..+. ...+|++.+++++++|++.++|||+++++.++|++
T Consensus 1 MI~~i~i~n~~G~~i~~k~y~~~~~~~~~~~~~~~~~~~~~~~--~~~~~i~~~~~~~~vy~~~~dl~~~~v~~~~eNel 78 (141)
T PF01217_consen 1 MIKAILILNSQGKRILSKYYRDVSEEERQKLFEKFIKKKSSRN--SKQSPIFEHDNYRIVYKRYSDLYFVVVGDENENEL 78 (141)
T ss_dssp SEEEEEEEETTSEEEEEEESSTSTSHHHHHHHHHHHHHHHTSS--SSSTSEEEETTEEEEEEEETTEEEEEEESSTSBHH
T ss_pred CEEEEEEEcCCCCEEEehhcCCccHHHHHHHHHHHHHHHHhcc--cccceeeecccceeeeEeeccEEEEEEeecccchH
Confidence 589999999999999999996554432 3444544444432 35689999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhcccccHHHHHhhHHHHHHHHHHHHhCCcccccCHHHHHHhhhcc
Q psy918 176 LVFVFLNKIVRVFTEYFKEIEEESIRDNFVVIYELLDELIDFGYPQTTDSKILQEYITQE 235 (504)
Q Consensus 176 ~~~~~L~~i~~vl~~y~~~l~e~~i~~n~~~i~~lldEiid~G~p~~t~~~~l~~~i~~~ 235 (504)
+++++|++++++|+.||++++|..|++||+.+|++||||+|+|+|++||++.|...+.+.
T Consensus 79 ~~~e~l~~~v~~l~~~~~~v~e~~i~~N~~~v~~~LDEiid~G~i~etd~~~I~~~v~~~ 138 (141)
T PF01217_consen 79 LLLEFLHRLVEVLDDYFGNVSEKDILENFDLVYLILDEIIDGGIILETDPNVILKRVTMQ 138 (141)
T ss_dssp HHHHHHHHHHHHHHHHHSS-SHHHHHHTHHHHHHHHHHHEETTEES--THHHHHHHHHHC
T ss_pred HHHHHHHHhhhhhhhhhccccHHHHHHCHHHHHHHHHHHHhCCEEEECCHHHHHHHHHHh
Confidence 999999999999999999999999999999999999999999999999999999988764
No 8
>KOG0938|consensus
Probab=99.84 E-value=1.1e-21 Score=190.71 Aligned_cols=118 Identities=18% Similarity=0.253 Sum_probs=100.6
Q ss_pred CccccccCCCccccccccccccCeEEeCCeEEEEEeeCCEEEEEEecCCCCeeee------------------ccccccc
Q psy918 1 MGVIEKFMPLPHDEKKRRECLTLSLQTSDCTFATSNIKPLSVVSLPRRMPTLRLV------------------SHEPGRN 62 (504)
Q Consensus 1 ~~~~~~f~~~~~~~~~~~~~~~Pv~~~~~~~~~~i~~~~l~~v~~t~~n~~~~~v------------------~ee~ir~ 62 (504)
+++.|.||.+ |+.+.+ .++||+++|+++|.|+|+.|||+||+|++|+|++++ +||+||+
T Consensus 26 rs~~diFRv~-vi~n~d--~r~PV~~igsttf~~~r~~nl~lvaitksN~Nva~v~eFl~kl~avm~aYfgk~~Eeaikn 102 (446)
T KOG0938|consen 26 RSIVDIFRVQ-VINNLD--VRSPVLTIGSTTFHHIRSSNLWLVAITKSNANVAAVFEFLYKLDAVMNAYFGKDREEAIKN 102 (446)
T ss_pred hhHHHHHHHh-hhhccc--cCCCeeEecceeEEEEeeccEEEEEEecCCCchhhHHHHHHHHHHHHHHHhcccchhhhhh
Confidence 5789999999 999944 789999999999999999999999999999999999 9999999
Q ss_pred c----------------------------cccccccce---------ecCCCC----cceecccccCCCC-----Cchhh
Q psy918 63 N----------------------------IHTGRTQAE---------IQPRIP----MAVTNAVSWPNNN-----NSILF 96 (504)
Q Consensus 63 n----------------------------i~~~~~~~~---------~~~~~~----~~~t~~v~Wr~~g-----Neif~ 96 (504)
| |++++.+.. .+.+++ +++||+|+||++| ||+||
T Consensus 103 nf~lI~ElLDemld~G~pqnte~~al~~~is~~~Vrs~g~~ls~k~s~~sq~~~~~ssqv~G~i~WRr~Gi~ykknevfl 182 (446)
T KOG0938|consen 103 NFVLIYELLDEMLDFGIPQNTEPNALKAQISQKGVRSMGGVLSSKSSPTSQATELRSSQVTGKIGWRREGIKYKKNEVFL 182 (446)
T ss_pred ceEeHHHHHHHHHhcCCCccCChhHHHhhhhhhhhhccccccCCcCCCCcccccccccccccccccccccceeccceeEe
Confidence 9 333332211 123555 7889999999999 99999
Q ss_pred hhheeeeEEEeCCCCeeeeeecccCc
Q psy918 97 IMSASALYILDVKGKVLISRNYRGDV 122 (504)
Q Consensus 97 dv~i~~~~i~~~~G~vl~~r~y~~~~ 122 (504)
|+.++.+++++++|++|.+ +..|.+
T Consensus 183 dvvErvNlLmS~~GnVLrs-~VsG~V 207 (446)
T KOG0938|consen 183 DVVERVNLLMSSDGNVLRS-DVSGTV 207 (446)
T ss_pred EehheeeeEEcCCCCEEEe-ecccEE
Confidence 9999999999999999988 545443
No 9
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=99.77 E-value=4.8e-18 Score=145.63 Aligned_cols=131 Identities=18% Similarity=0.322 Sum_probs=117.5
Q ss_pred heeeeEEEeCCCCeeeeeecccCcc---hhHHHHHHHHhhcccccCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCccHH
Q psy918 99 SASALYILDVKGKVLISRNYRGDVE---MGVIEKFMPLLMEKEEEGMLTPLLQTSDCTFAYIKYNNLFIVSTTKKNANIA 175 (504)
Q Consensus 99 ~i~~~~i~~~~G~vl~~r~y~~~~~---~~~~~~f~~~v~~~~~~~~~~pv~~~~~~~~v~~~~~~ly~v~~~~~~~n~l 175 (504)
|+.+++|+|++|++++.|||..... ..+....+..+.+++. +++.+++..+.+.+|+++++|||+++.+.+.|++
T Consensus 1 ~i~~vli~nrqgk~RL~K~yt~~~~~e~~kli~~i~~lIs~R~~--ke~N~~e~k~~kiVYrrYA~LyF~f~Vd~~dnEl 78 (152)
T COG5030 1 MIKFVLIFNRQGKPRLVKWYTPVSDPEQAKLIADIYELISARKP--KESNFIEGKNEKIVYRRYATLYFVFGVDNDDNEL 78 (152)
T ss_pred CeEEEEEEcCCCceeeeEeeccCCcHHHHHHHHHHHHHHHcCCc--hhcccccccCcEEEeeecCcEEEEEEEcCCCCcc
Confidence 4789999999999999999986332 2467778888887753 5788999998899999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhcccccHHHHHhhHHHHHHHHHHHHhCCcccccCHHHHHHh
Q psy918 176 LVFVFLNKIVRVFTEYFKEIEEESIRDNFVVIYELLDELIDFGYPQTTDSKILQEY 231 (504)
Q Consensus 176 ~~~~~L~~i~~vl~~y~~~l~e~~i~~n~~~i~~lldEiid~G~p~~t~~~~l~~~ 231 (504)
.+++++|.|+++|+.|||+++|.++..||..+|.+||||+-+|..++++++.+.+.
T Consensus 79 ~iL~lIh~FVE~lDr~FgnVCELdlIFNF~kv~~ILdE~i~gG~i~Es~~~~vl~~ 134 (152)
T COG5030 79 IILELIHNFVEILDRFFGNVCELDLIFNFQKVYAILDEMILGGEIIESSKNEVLEH 134 (152)
T ss_pred hHHHHHHHHHHHHHHHhccceeeEeEeeHHHHHHHHHHHHhCCeeeecCHHHHHHH
Confidence 99999999999999999999999999999999999999999999999998765443
No 10
>KOG0937|consensus
Probab=99.70 E-value=5.8e-18 Score=172.01 Aligned_cols=121 Identities=30% Similarity=0.366 Sum_probs=105.6
Q ss_pred CccccccCCCccccccccccccCeEEeCCeEEEEEeeCCEEEEEEecCCCCeeee------------------ccccccc
Q psy918 1 MGVIEKFMPLPHDEKKRRECLTLSLQTSDCTFATSNIKPLSVVSLPRRMPTLRLV------------------SHEPGRN 62 (504)
Q Consensus 1 ~~~~~~f~~~~~~~~~~~~~~~Pv~~~~~~~~~~i~~~~l~~v~~t~~n~~~~~v------------------~ee~ir~ 62 (504)
++++|.|+.+ +...++.+..+|++.++|.+|+|++|++||+||++|.|++|+++ +|+++||
T Consensus 25 ~s~~~~F~~~-l~~~e~~~~~~p~l~~~g~~~~~ik~s~lylv~~~~~n~~a~~v~~~l~~~~~v~~~y~~~l~e~si~~ 103 (424)
T KOG0937|consen 25 MSSTEKFFRK-LFEKEEGDESPPFLVHDGSRFIHIKHSNLYLVAGTRPNVSAALVLSFLYAVADVFGDYLSELEEESIRD 103 (424)
T ss_pred hhhhhhHHHH-HhhhcccCCCCCeEEeCCceEEEEeecceEEEEEeccCCCHHHHHHHHHHHHHHHHHHhccCCccceec
Confidence 4678999988 77776555789999999999999999999999999999999999 7999999
Q ss_pred c----------------------------cccccccceec-CCCCcceecccccCCCC-----CchhhhhheeeeEEEeC
Q psy918 63 N----------------------------IHTGRTQAEIQ-PRIPMAVTNAVSWPNNN-----NSILFIMSASALYILDV 108 (504)
Q Consensus 63 n----------------------------i~~~~~~~~~~-~~~~~~~t~~v~Wr~~g-----Neif~dv~i~~~~i~~~ 108 (504)
| |++++++++.. +++|+++|++++||++| ||+||||+++..+++++
T Consensus 104 n~vlvyElLde~mDFGypQ~t~s~iL~~yi~~~~~~l~~~~~~~p~avtnavsWrs~gi~~~KnevflDViE~Vs~l~~~ 183 (424)
T KOG0937|consen 104 NFVLVYELLDEVMDFGYPQTTDSEILKNYITQKANRLQDAQPRPPLAVTNAVSWRSEGIYYGKNEVFLDVIESVSLLYDS 183 (424)
T ss_pred chHHHHHHHHHHhccCCcccchHHHHHHHhcccccceeecCCCCCcccccceeecccccccccceEEEEhhhhhhHhhhc
Confidence 9 77888887653 37899999999999999 99999997777899999
Q ss_pred CCCeeeeeecccCcc
Q psy918 109 KGKVLISRNYRGDVE 123 (504)
Q Consensus 109 ~G~vl~~r~y~~~~~ 123 (504)
+|.++.+ ...|.+.
T Consensus 184 ~G~vl~s-~i~G~I~ 197 (424)
T KOG0937|consen 184 NGIVLLS-EIVGTIK 197 (424)
T ss_pred CCcEEEe-eeeeEEE
Confidence 9999988 4444443
No 11
>KOG3343|consensus
Probab=99.69 E-value=2.1e-16 Score=138.58 Aligned_cols=137 Identities=20% Similarity=0.298 Sum_probs=126.7
Q ss_pred eeeeEEEeCCCCeeeeeecccCcch--hHHHHHHHHhhcccccCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCccHHHH
Q psy918 100 ASALYILDVKGKVLISRNYRGDVEM--GVIEKFMPLLMEKEEEGMLTPLLQTSDCTFAYIKYNNLFIVSTTKKNANIALV 177 (504)
Q Consensus 100 i~~~~i~~~~G~vl~~r~y~~~~~~--~~~~~f~~~v~~~~~~~~~~pv~~~~~~~~v~~~~~~ly~v~~~~~~~n~l~~ 177 (504)
+.+++|+|++|+.+.+|||.++++. ....+|.+.+.+++++ ....|..++|...+|+..-||+|..+...++|+++.
T Consensus 9 vk~iliLD~~G~Ri~aKYY~~~~~s~vkeqkaFEK~lF~KT~k-t~~eI~~ldg~~vvYk~~~Dl~fyv~G~~~ENEl~L 87 (175)
T KOG3343|consen 9 VKAILILDSDGKRILAKYYDDPHPSTVKEQKAFEKNLFSKTSK-TESEILLLDGNTVVYKSVIDLHFYVVGSEEENELML 87 (175)
T ss_pred hheEEEEcCCCCEeeeeecCCCcchhHHHHHHHHHHHhccccc-ccceeEEecCcEEEEEecccEEEEEecCcchhHHHH
Confidence 5789999999999999999998876 3578899999988764 778899999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhcc-cccHHHHHhhHHHHHHHHHHHHhCCcccccCHHHHHHhhhccCc
Q psy918 178 FVFLNKIVRVFTEYFK-EIEEESIRDNFVVIYELLDELIDFGYPQTTDSKILQEYITQEGH 237 (504)
Q Consensus 178 ~~~L~~i~~vl~~y~~-~l~e~~i~~n~~~i~~lldEiid~G~p~~t~~~~l~~~i~~~~~ 237 (504)
.+.|+++.+.+.-.++ +++...+.+|++.|...+|||||+|.+++||++++...+...+.
T Consensus 88 ~svL~~l~dal~llLr~nveKr~llEN~D~i~L~~DEiiD~GvILEtdp~~ia~rv~~~~~ 148 (175)
T KOG3343|consen 88 MSVLTCLFDALSLLLRKNVEKRELLENLDLIFLALDEIIDGGVILETDPNQIAQRVALRPT 148 (175)
T ss_pred HHHHHHHHHHHHHHHHhChhHHHHHhhhccceeehhhhccCceEEecCHHHHHHHhccCCC
Confidence 9999999999999996 48889999999999999999999999999999999999887664
No 12
>KOG0934|consensus
Probab=99.68 E-value=7e-17 Score=138.40 Aligned_cols=127 Identities=20% Similarity=0.315 Sum_probs=113.1
Q ss_pred heeeeEEEeCCCCeeeeeecccCcc--h-hHHHHHHHHhhcccccCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCccHH
Q psy918 99 SASALYILDVKGKVLISRNYRGDVE--M-GVIEKFMPLLMEKEEEGMLTPLLQTSDCTFAYIKYNNLFIVSTTKKNANIA 175 (504)
Q Consensus 99 ~i~~~~i~~~~G~vl~~r~y~~~~~--~-~~~~~f~~~v~~~~~~~~~~pv~~~~~~~~v~~~~~~ly~v~~~~~~~n~l 175 (504)
|+...++++++|++.++|||..... | .......+.++++. .+++.+++..+.+.||++++.|||+|....+.|+|
T Consensus 1 mi~f~LlvsrQGk~rL~k~y~~~~~~er~~i~re~i~~~Lar~--pk~csfie~kd~kvVyrryasl~f~~~v~~~dNEL 78 (145)
T KOG0934|consen 1 MIKFFLLVSRQGKTRLQKWYEALSIKERKKIERELIKSVLARK--PKMCSFIEYKDEKVVYRRYASLFFCVGVEDNDNEL 78 (145)
T ss_pred CeEEEEEEeccCceehhHHHhhhcHHHHHHHHHHHHHHHHhCC--cccccchhccCceehhhhhhhEEEEEEEecCCchh
Confidence 4788999999999999999986433 2 34566667777664 46889999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhcccccHHHHHhhHHHHHHHHHHHHhCCcccccCHHH
Q psy918 176 LVFVFLNKIVRVFTEYFKEIEEESIRDNFVVIYELLDELIDFGYPQTTDSKI 227 (504)
Q Consensus 176 ~~~~~L~~i~~vl~~y~~~l~e~~i~~n~~~i~~lldEiid~G~p~~t~~~~ 227 (504)
.++|++|+++++|+.|||+++|.+|..||..+|.+|||++-.|..+++..+.
T Consensus 79 ~~LE~IH~~vE~lDkYFg~VCELDiiFNfekay~ILde~~~~g~~~e~~k~~ 130 (145)
T KOG0934|consen 79 AILEFIHNYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEIQETSKND 130 (145)
T ss_pred hHHHHHHHHHHHHHHHhccceeeEEEEehHhHHHHHHHHhcCcchHhhhccc
Confidence 9999999999999999999999999999999999999999999988888653
No 13
>KOG0935|consensus
Probab=99.62 E-value=3.5e-15 Score=124.67 Aligned_cols=132 Identities=18% Similarity=0.265 Sum_probs=108.5
Q ss_pred heeeeEEEeCCCCeeeeeecccCcc--h-hHHHHHHHHhhcccccCCCCCEEEeCCEE-EEEEEeCCEEEEEEecCCccH
Q psy918 99 SASALYILDVKGKVLISRNYRGDVE--M-GVIEKFMPLLMEKEEEGMLTPLLQTSDCT-FAYIKYNNLFIVSTTKKNANI 174 (504)
Q Consensus 99 ~i~~~~i~~~~G~vl~~r~y~~~~~--~-~~~~~f~~~v~~~~~~~~~~pv~~~~~~~-~v~~~~~~ly~v~~~~~~~n~ 174 (504)
|+..++|.|.+|+..++|||.+-.. + .+.+...+.+..++. +....++....+ .+++++++|||+...+...|+
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 4788999999999999999975322 3 356667777766653 333444444344 444699999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhcccccHHHHHhhHHHHHHHHHHHHhCCcccccCHHHHHHhh
Q psy918 175 ALVFVFLNKIVRVFTEYFKEIEEESIRDNFVVIYELLDELIDFGYPQTTDSKILQEYI 232 (504)
Q Consensus 175 l~~~~~L~~i~~vl~~y~~~l~e~~i~~n~~~i~~lldEiid~G~p~~t~~~~l~~~i 232 (504)
+..++.+|.|+++|+.||++++|.++..||-.+|.++|||+-+|.+++|+...+-+.+
T Consensus 79 layLe~IHlFVEvLd~fF~NVCELDlvFNFyKVy~i~DEm~l~GEi~Etsk~~vlerl 136 (143)
T KOG0935|consen 79 LAYLEHIHLFVEVLDEFFHNVCELDLVFNFYKVYTIVDEMFLAGEIRETSKTKVLERL 136 (143)
T ss_pred HHHHHHHHHHHHHHHHHhccccceeeeeeeeeHHHHHHHHHHhhhhhhhhHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999987665544
No 14
>KOG0936|consensus
Probab=99.59 E-value=1.7e-14 Score=125.44 Aligned_cols=134 Identities=18% Similarity=0.274 Sum_probs=115.8
Q ss_pred heeeeEEEeCCCCeeeeeecccCc-c--hhHHHHHHHHhhcccccCCCCCEEE------eCCEEEEEEEeCCEEEEEEec
Q psy918 99 SASALYILDVKGKVLISRNYRGDV-E--MGVIEKFMPLLMEKEEEGMLTPLLQ------TSDCTFAYIKYNNLFIVSTTK 169 (504)
Q Consensus 99 ~i~~~~i~~~~G~vl~~r~y~~~~-~--~~~~~~f~~~v~~~~~~~~~~pv~~------~~~~~~v~~~~~~ly~v~~~~ 169 (504)
||.+++|+|.+|++++.|.|.... + ..+++.-+..+.++++ ..+.+++ -.+.+.+|+.+..|||+.+.+
T Consensus 1 MI~AvlifNn~gkPRL~KFY~p~~~~~Qq~lir~vf~lvs~R~~--n~~nFLe~~~l~g~~d~rlIYrhYATLYFvfvvD 78 (182)
T KOG0936|consen 1 MIKAVLIFNNKGKPRLVKFYTPVDEEKQQQLIREVFHLVSKRPD--NVCNFLEGNSLIGGSDNRLIYRHYATLYFVFVVD 78 (182)
T ss_pred CeeEEEEecCCCCcceeeecCcCChHHHHHHHHHHHHHHHcCCc--hHhhhhccccccCCccceeehheeeeEEEEEEEc
Confidence 589999999999999999998633 2 2467777777777753 3444544 235789999999999999999
Q ss_pred CCccHHHHHHHHHHHHHHHHhhcccccHHHHHhhHHHHHHHHHHHHhCCcccccCHHHHHHhhhc
Q psy918 170 KNANIALVFVFLNKIVRVFTEYFKEIEEESIRDNFVVIYELLDELIDFGYPQTTDSKILQEYITQ 234 (504)
Q Consensus 170 ~~~n~l~~~~~L~~i~~vl~~y~~~l~e~~i~~n~~~i~~lldEiid~G~p~~t~~~~l~~~i~~ 234 (504)
+.+++|.++++++-|++.|+.+|..++|.++..|+..++.+|+|++.+|..++|+.+.+..-+..
T Consensus 79 ~sEsEL~iLDLIQvfVEtLDkCF~nVcELDliF~~~k~h~iL~EiV~GGmVlETn~neIv~av~~ 143 (182)
T KOG0936|consen 79 SSESELGILDLIQVFVETLDKCFENVCELDLIFNWQKVHAILAEIVMGGMVLETNMNEIVAAVDE 143 (182)
T ss_pred CCcchhHHHHHHHHHHHHHHHHHHhhhhhhheeeHHHHHHHHHHHHhCCeEEeccHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999887666654
No 15
>KOG2740|consensus
Probab=99.22 E-value=8.1e-12 Score=123.50 Aligned_cols=120 Identities=14% Similarity=0.178 Sum_probs=97.3
Q ss_pred CccccccCCCccccccccccccCeEEeCCeEEEE-EeeCCEEEEEEecCCCCeeee------------------cccccc
Q psy918 1 MGVIEKFMPLPHDEKKRRECLTLSLQTSDCTFAT-SNIKPLSVVSLPRRMPTLRLV------------------SHEPGR 61 (504)
Q Consensus 1 ~~~~~~f~~~~~~~~~~~~~~~Pv~~~~~~~~~~-i~~~~l~~v~~t~~n~~~~~v------------------~ee~ir 61 (504)
|++|+.|+.. -....+.+..+||+.. .++|++ +-++++||||++...+.|+++ +|..|+
T Consensus 27 rsic~~f~e~-~~~~~~~e~~ppvi~~-p~hylfsv~~~~i~~~~~st~e~pPL~~iefL~rv~dv~~eyFg~~s~~~Ik 104 (418)
T KOG2740|consen 27 RSICDYFFED-QSSDDDLEHVPPVIST-PHHYLFSVYRDLIFFCAVSTVETPPLMVIEFLHRVVDVLLEYFGGLSESKIK 104 (418)
T ss_pred eehHHHHHHh-hhhccccccCCceecC-CceeeeeeeccCcEEEEEEeccCCChhHHHHHHHHHHHHHHHhcccCHhHhh
Confidence 5788888888 5555555578888876 666666 999999999999999999999 999999
Q ss_pred cc-----------------ccccccccee---------------------cCCCCcceecccccCCCC-----Cchhhhh
Q psy918 62 NN-----------------IHTGRTQAEI---------------------QPRIPMAVTNAVSWPNNN-----NSILFIM 98 (504)
Q Consensus 62 ~n-----------------i~~~~~~~~~---------------------~~~~~~~~t~~v~Wr~~g-----Neif~dv 98 (504)
|| ..+|++.+++ +.++|+++-+.||||+.| ||.|+|+
T Consensus 105 ~N~~vv~ell~emiDnGfpl~tE~NiLke~i~pps~l~~~~~svTg~~n~~~~lPtg~~s~VPWR~~~~Ky~nNE~yvdv 184 (418)
T KOG2740|consen 105 DNVVVVYELLDEMIDNGFPLVTEPNILKELIPPPSFLSKKFNSVTGNSNVSDTLPTGALSNVPWRTAGVKYTNNEAYVDV 184 (418)
T ss_pred cceeeHHHHHHHHHHcCCCcccChhHHHhhcCChHHHHHHHhhhhccccccccCCCcccccccccccCcccccchhhhhh
Confidence 99 5566666542 347888888899999999 9999999
Q ss_pred heeeeEEEeCCCCeeeeeecccCcc
Q psy918 99 SASALYILDVKGKVLISRNYRGDVE 123 (504)
Q Consensus 99 ~i~~~~i~~~~G~vl~~r~y~~~~~ 123 (504)
.++...|++++|..+.. ...|++.
T Consensus 185 lEeidai~~k~gslv~~-eI~g~vd 208 (418)
T KOG2740|consen 185 LEEIDAIVDKKGSLVFG-EIQGIVD 208 (418)
T ss_pred hheeheEecCCCCEEEE-EEEEEEE
Confidence 88889999999997766 4444433
No 16
>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=99.20 E-value=5.6e-11 Score=104.11 Aligned_cols=137 Identities=19% Similarity=0.236 Sum_probs=121.0
Q ss_pred eeeeEEEeCCCCeeeeeecccCcchh----------HHHHHHHHhhcccccCCCCCEEEeCCEEEEEEEeCCEEEEEEec
Q psy918 100 ASALYILDVKGKVLISRNYRGDVEMG----------VIEKFMPLLMEKEEEGMLTPLLQTSDCTFAYIKYNNLFIVSTTK 169 (504)
Q Consensus 100 i~~~~i~~~~G~vl~~r~y~~~~~~~----------~~~~f~~~v~~~~~~~~~~pv~~~~~~~~v~~~~~~ly~v~~~~ 169 (504)
+++++|+|++|+++..|+|.+.+.+. -.+.|.+.+...+. +.+..|...++.-.++.+..++.|..+..
T Consensus 8 v~a~LilDsqGeriy~kyy~pph~~eg~~~vFnsvkkekefek~l~eKt~-k~~~~Il~f~d~lV~~k~~~dv~~yiv~~ 86 (187)
T COG5541 8 VEALLILDSQGERIYRKYYQPPHRSEGHQLVFNSVKKEKEFEKKLAEKTA-KDRESILMFYDRLVMCKRLDDVLLYIVSP 86 (187)
T ss_pred eeeeEEecCCccchhhhhcCCcccccccchhhcchhHHHHHHHHHHHHhh-cCccceeeEcceeeeeeeehhEEEEEecc
Confidence 48899999999999999998765531 36778888876654 46788999999999999999999999998
Q ss_pred CCccHHHHHHHHHHHHHHHHhhccc-ccHHHHHhhHHHHHHHHHHHHhCCcccccCHHHHHHhhhccCc
Q psy918 170 KNANIALVFVFLNKIVRVFTEYFKE-IEEESIRDNFVVIYELLDELIDFGYPQTTDSKILQEYITQEGH 237 (504)
Q Consensus 170 ~~~n~l~~~~~L~~i~~vl~~y~~~-l~e~~i~~n~~~i~~lldEiid~G~p~~t~~~~l~~~i~~~~~ 237 (504)
-++|+.++.+.+..|..+|.-.++. .++..+.+|++.|..++||.||.|.+.+|+++.+.+.++.+++
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 9999999999999999999999976 5667799999999999999999999999999999999987654
No 17
>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=98.84 E-value=4.6e-07 Score=89.59 Aligned_cols=204 Identities=18% Similarity=0.251 Sum_probs=111.7
Q ss_pred EEEEEEEeEEEEEccCCceEEEEEEEEEEEEEEeC------CCCeEEEEecCcccccccCCCCCCceeeccccccccccc
Q psy918 267 VFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLS------GMPELRLGLNDKVLFESTGRGKSKSVELEDVKFHQCVRL 340 (504)
Q Consensus 267 I~vdV~E~v~~~~~~~G~v~~~~V~G~I~~ks~Ls------G~P~~~l~Ln~~~~~~~~~~~~~~~i~l~d~~fH~cV~~ 340 (504)
+-..|.|.|||.+. +|.+.++.|.|+|.+.---. ..+.+.+.|++... |+.+.-.+..=.
T Consensus 3 l~asi~E~VnA~Fk-~g~~~~v~v~GEv~ls~~~~~~~~~~~~~~l~~rl~n~~~-------------le~i~pN~~~v~ 68 (257)
T PF10291_consen 3 LNASITETVNAYFK-GGQLSKVKVTGEVALSYPAGISSSLTSPPPLSFRLNNFSR-------------LEKIAPNPQFVS 68 (257)
T ss_dssp EEEEEEEEEEEEEE-TTEEEEEEEEEEEEEEEE--SSS-----SEEEEEEETGGG-------------EEEEEE-TTTE-
T ss_pred eeEEEEEEEEEEEE-CCcEEEEEEEEEEEEecCCChhhcccCCCcEEEEEcCcch-------------hceeecCHhHee
Confidence 55679999999985 57788999999999873221 23567888876542 222222211110
Q ss_pred cCcCCCceEEEeCC--CCce--eEEEEEecCC----CCCceEEEEEEE-ecccEEEEEEEEeec-cCCCccccceEEEEe
Q psy918 341 SRFENDRTISFIPP--DGEF--ELMSYRLNTH----VKPLIWIESVIE-RFVHSRVEYMIKAKS-QFKRRSTANNVEIVI 410 (504)
Q Consensus 341 ~~f~~~r~i~F~PP--dG~F--~Lm~Yr~~~~----~~~P~~i~~~~~-~~~~~~le~~l~l~~-~~~~~~~~~~v~I~i 410 (504)
..-.++....|.++ .... ..|+|++... ...|+.+.+.-. +.....+-+..++.+ .+......+||.|.+
T Consensus 69 ~~~~~~~~f~~n~~~l~~~~~~~alKYqv~~~~~~~~~~Pl~l~~~Wk~e~~~tsl~l~Y~~Np~~~~~~~~L~nv~~~v 148 (257)
T PF10291_consen 69 SSSQSDGEFWLNMSALTSHLPKQALKYQVHSDPSNLSSVPLILKPVWKCEPSQTSLILDYKLNPDAFASPVPLENVVFSV 148 (257)
T ss_dssp -EEEETTEEEE-TTTTBT-E-EEEEEEEEES--------SEEEEEEEEE-SSEEEEEEEEEE-TTT--E-EEEEEEEEEE
T ss_pred cCCCCCCcEEEehHHhhhhhhhceEEEEEeccccccCCCCeEEEeEEEeCCceEEEEEEEEeChhhccccceeeeEEEEE
Confidence 01112233555544 2333 5699999863 457887776433 333344444445555 444446789999999
Q ss_pred cCCCC-CCCCeEEeeeeEEEEeCCCcEEEEEeceec--CCce-EEEEEEEEecCCCCCCCCCCCCEEEEEEEC-Cccccc
Q psy918 411 PVPAD-ADSPKFKTTIGSVKYTPEQSAITWTIKSFP--GGKE-YLMRAHFGLPSVENEDAEGKPPIQVKFEIP-YFTTSG 485 (504)
Q Consensus 411 P~P~~-~~~~~~~~s~G~~~~~~~~~~lvW~I~k~~--g~~~-~~l~~~~~l~s~~~~~~~~~~pi~v~F~ip-~~t~SG 485 (504)
++... ..+++ +.-.+.|..+++.+.|+++.+. ++.+ ..|.|+|...... ..-+++.++|++. .-+.||
T Consensus 149 ~l~g~~~ts~~---skP~g~~~~e~~ri~Wrl~el~~~~~~~~~kL~ARf~~~~~~----~~p~~v~vkF~~~~~~~~sg 221 (257)
T PF10291_consen 149 PLDGGRATSAQ---SKPQGTWNKEKNRITWRLPELSLTSEGEGGKLIARFMTSGGP----SRPGGVEVKFEIEGGSTLSG 221 (257)
T ss_dssp EB-SS-EEEEE---ESSS--B-SSS-EEEEE-SSEEEETT---EEEEEEEEESS--------SS-EEEEEEE---S-SS-
T ss_pred EcCCccccccc---cCCCccccCCCcEEEEECCcccccCCCCCceEEEEEECCCCC----CCCceEEEEEEEcCCCcccC
Confidence 99776 32222 3334678899999999999765 3333 6899999876532 2567899999999 888999
Q ss_pred eEEEEE
Q psy918 486 IQVRYL 491 (504)
Q Consensus 486 l~V~~l 491 (504)
+.|.-+
T Consensus 222 ~~i~~~ 227 (257)
T PF10291_consen 222 LGISLV 227 (257)
T ss_dssp ---EEE
T ss_pred cEEEEe
Confidence 888877
No 18
>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=95.45 E-value=0.012 Score=52.76 Aligned_cols=44 Identities=11% Similarity=0.012 Sum_probs=41.5
Q ss_pred cccCeEEeCCeEEEEEeeCCEEEEEEecCCCCeeee------------------cccccccc
Q psy918 20 CLTLSLQTSDCTFATSNIKPLSVVSLPRRMPTLRLV------------------SHEPGRNN 63 (504)
Q Consensus 20 ~~~Pv~~~~~~~~~~i~~~~l~~v~~t~~n~~~~~v------------------~ee~ir~n 63 (504)
..+|++.++++.++|.+.++|||++++..|.|++++ +|..|++|
T Consensus 45 ~~~~i~~~~~~~~vy~~~~dl~~~~v~~~~eNel~~~e~l~~~v~~l~~~~~~v~e~~i~~N 106 (141)
T PF01217_consen 45 KQSPIFEHDNYRIVYKRYSDLYFVVVGDENENELLLLEFLHRLVEVLDDYFGNVSEKDILEN 106 (141)
T ss_dssp SSTSEEEETTEEEEEEEETTEEEEEEESSTSBHHHHHHHHHHHHHHHHHHHSS-SHHHHHHT
T ss_pred ccceeeecccceeeeEeeccEEEEEEeecccchHHHHHHHHHhhhhhhhhhccccHHHHHHC
Confidence 458999999999999999999999999999999988 89999999
No 19
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=94.29 E-value=0.3 Score=45.76 Aligned_cols=80 Identities=13% Similarity=0.147 Sum_probs=70.3
Q ss_pred EEEEEEEeCCEEEEEEecCCccHHHHHHHHHHHHHHHHhhcccccH-HHHHhhHHHHHHHHHHHHhCCcccccCHHHHHH
Q psy918 152 CTFAYIKYNNLFIVSTTKKNANIALVFVFLNKIVRVFTEYFKEIEE-ESIRDNFVVIYELLDELIDFGYPQTTDSKILQE 230 (504)
Q Consensus 152 ~~~v~~~~~~ly~v~~~~~~~n~l~~~~~L~~i~~vl~~y~~~l~e-~~i~~n~~~i~~lldEiid~G~p~~t~~~~l~~ 230 (504)
..++.....++-|+.+++..+|.+++-.||+.++..|.+.+..++- ..+....+.|..+|+..++.|.-.-.+.+.+|.
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 4678889999999999999999999999999999999999976544 667789999999999999999988888776654
Q ss_pred h
Q psy918 231 Y 231 (504)
Q Consensus 231 ~ 231 (504)
+
T Consensus 184 l 184 (189)
T PF15001_consen 184 L 184 (189)
T ss_pred H
Confidence 3
No 20
>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=93.13 E-value=0.04 Score=54.51 Aligned_cols=38 Identities=29% Similarity=0.521 Sum_probs=30.4
Q ss_pred cccCCCC-----CchhhhhheeeeEEEeCCCCeeeeeecccCcc
Q psy918 85 VSWPNNN-----NSILFIMSASALYILDVKGKVLISRNYRGDVE 123 (504)
Q Consensus 85 v~Wr~~g-----Neif~dv~i~~~~i~~~~G~vl~~r~y~~~~~ 123 (504)
++||..| ||||+||.+...++++.+|.++.+ .-+|.+.
T Consensus 1 ~~wR~~~~~~~~nei~vdv~E~i~~~~~~~G~~~~~-~v~G~v~ 43 (262)
T PF00928_consen 1 VPWRPSGIKYKKNEIFVDVVEKISAVLDRDGNILSS-EVKGSVQ 43 (262)
T ss_dssp -TTS-STB--SSEEEEEEEEEEEEEEEETTSEEEEE-EEEEEEE
T ss_pred CCcccCCcccccceEEEEEEEEEEEEEccCCcEEEE-EEEEEEE
Confidence 6899999 999999977778999999998888 4555544
No 21
>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=90.89 E-value=2.1 Score=45.46 Aligned_cols=88 Identities=19% Similarity=0.342 Sum_probs=58.5
Q ss_pred eeeeEEEeCCCCeeeeeecccCcch-----hHHHHHHHHhhcccccCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCccH
Q psy918 100 ASALYILDVKGKVLISRNYRGDVEM-----GVIEKFMPLLMEKEEEGMLTPLLQTSDCTFAYIKYNNLFIVSTTKKNANI 174 (504)
Q Consensus 100 i~~~~i~~~~G~vl~~r~y~~~~~~-----~~~~~f~~~v~~~~~~~~~~pv~~~~~~~~v~~~~~~ly~v~~~~~~~n~ 174 (504)
-.-+||++.-|+++.+|+ |+-.. ++..++...+... ++.---+..++.++++..++.||+||+++..+++
T Consensus 11 ~kh~fIlS~AGKPIysr~--G~e~~l~~~~g~~~aiiS~~~~~---~d~l~~i~~~~~~ivfl~r~pl~lv~vS~~~e~~ 85 (415)
T PF03164_consen 11 KKHFFILSSAGKPIYSRY--GDEDKLSSLMGVIQAIISFFQSN---GDELRSIRAGDHRIVFLNRGPLILVAVSKTGESE 85 (415)
T ss_pred CCeEEEECCCCceeEEec--CChHHHHHHHHHHHHHHHHHHhC---CCcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCH
Confidence 456899999999999977 33222 2333333222211 2233356788999999999999999999998887
Q ss_pred HHHHHHHHHHHHHHHhhc
Q psy918 175 ALVFVFLNKIVRVFTEYF 192 (504)
Q Consensus 175 l~~~~~L~~i~~vl~~y~ 192 (504)
..+..-|+.+...|-..+
T Consensus 86 ~~l~~qL~~ly~qils~l 103 (415)
T PF03164_consen 86 SQLRKQLDYLYSQILSIL 103 (415)
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 766555555555444443
No 22
>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=88.36 E-value=3.9 Score=32.78 Aligned_cols=50 Identities=18% Similarity=0.351 Sum_probs=42.7
Q ss_pred CCEEEeCCEEEEEEEeCCEEEEEEecCCccHHHHHHHHHHHHHHHHhhcc
Q psy918 144 TPLLQTSDCTFAYIKYNNLFIVSTTKKNANIALVFVFLNKIVRVFTEYFK 193 (504)
Q Consensus 144 ~pv~~~~~~~~v~~~~~~ly~v~~~~~~~n~l~~~~~L~~i~~vl~~y~~ 193 (504)
.-.++.++..|-+...+++.++|+++.+-+.-.++.||+.+.+-...-++
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 34677888888888899999999999999999999999999988887776
No 23
>KOG0859|consensus
Probab=87.81 E-value=18 Score=34.12 Aligned_cols=88 Identities=16% Similarity=0.267 Sum_probs=64.0
Q ss_pred eEEEeCCCCeeeeeecccCcc--hhHHHHHHHHhhcccccCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCccHHHHHHH
Q psy918 103 LYILDVKGKVLISRNYRGDVE--MGVIEKFMPLLMEKEEEGMLTPLLQTSDCTFAYIKYNNLFIVSTTKKNANIALVFVF 180 (504)
Q Consensus 103 ~~i~~~~G~vl~~r~y~~~~~--~~~~~~f~~~v~~~~~~~~~~pv~~~~~~~~v~~~~~~ly~v~~~~~~~n~l~~~~~ 180 (504)
++-+=++|.++++.+ ..-.. .++.+....++-.. ++..=-+..|++.|-|...+++.++|+++.+.--...+.|
T Consensus 4 iYs~VARGTvvLaef-t~~~gNf~sva~qiL~klp~~---~n~k~tYs~d~y~Fh~l~~dg~tylcvadds~gR~ipfaF 79 (217)
T KOG0859|consen 4 IYSFVARGTVILAEF-TEFSGNFSSIAAQILQKLPSS---SNSKFTYSCDGYTFHYLVEDGLTYLCVADDSAGRQIPFAF 79 (217)
T ss_pred eEEEEecceEEEEee-eeccCCHHHHHHHHHHhCCCC---CCCceEEecCCeEEEEEEeCCeEEEEEEeccccccccHHH
Confidence 344557999999954 32211 24566666666432 2334567899999999999999999999988887888999
Q ss_pred HHHHHHHHHhhccc
Q psy918 181 LNKIVRVFTEYFKE 194 (504)
Q Consensus 181 L~~i~~vl~~y~~~ 194 (504)
|+++.+=+..-.|.
T Consensus 80 Le~Ik~~F~k~YG~ 93 (217)
T KOG0859|consen 80 LERIKEDFKKRYGG 93 (217)
T ss_pred HHHHHHHHHHHhcc
Confidence 99998877666654
No 24
>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=83.48 E-value=12 Score=32.58 Aligned_cols=91 Identities=14% Similarity=0.182 Sum_probs=61.1
Q ss_pred eeeeEEEeCCCCeeeeeecccCcch-----hHHHHHHHHhhcccc--cCCCC-CEEEeCCEEEEEEEeCCEEEEEEecCC
Q psy918 100 ASALYILDVKGKVLISRNYRGDVEM-----GVIEKFMPLLMEKEE--EGMLT-PLLQTSDCTFAYIKYNNLFIVSTTKKN 171 (504)
Q Consensus 100 i~~~~i~~~~G~vl~~r~y~~~~~~-----~~~~~f~~~v~~~~~--~~~~~-pv~~~~~~~~v~~~~~~ly~v~~~~~~ 171 (504)
+.+++|.|++|=++.. ...++.+. .....|-...-+-++ -++.. -+..++++.+++.....+|+..+++.+
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 LQAIVITDRDGVPIAK-VSSDSAPESAMRPSLLSTFAMAIDQASKLGLGKNKSIIAYYDSYQVVQFNKLPLYITFIASSN 95 (119)
T ss_dssp EEEEEEEETTS-EEEE-EE-TTS-GGGGSHHHHCCHHHHHHHHTTSSS-SEEEEEEEESSEEEEEEEETTEEEEEEEETT
T ss_pred eEEEEEECCCCcEEEE-ecCCCCcchhhhhHHHHHHHHHhhcccccCCCCceEEEEEeCCEEEEEEeCCCeEEEEEecCC
Confidence 4788999999998887 43333332 122233332222111 12333 456789999999999999999999999
Q ss_pred ccHHHHHHHHHHHHHHHHhh
Q psy918 172 ANIALVFVFLNKIVRVFTEY 191 (504)
Q Consensus 172 ~n~l~~~~~L~~i~~vl~~y 191 (504)
.|.-+++++-+.+..++.+.
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 99999999999998888763
No 25
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=70.52 E-value=68 Score=27.53 Aligned_cols=89 Identities=15% Similarity=0.309 Sum_probs=54.3
Q ss_pred hheeeeEEEeCCCCeeeeeecccCcch---h-------H---HHHHHHHhhcccccCCCCC--EEEeCCE-EEEEEEeCC
Q psy918 98 MSASALYILDVKGKVLISRNYRGDVEM---G-------V---IEKFMPLLMEKEEEGMLTP--LLQTSDC-TFAYIKYNN 161 (504)
Q Consensus 98 v~i~~~~i~~~~G~vl~~r~y~~~~~~---~-------~---~~~f~~~v~~~~~~~~~~p--v~~~~~~-~~v~~~~~~ 161 (504)
|.+++++|+|+.|..+..|+|..+..+ + . ..++..++.-.. + .++ +++.+.. -++|+...+
T Consensus 1 mave~~~iINksGglifqref~~~et~lnsneyLiLastlhgV~aI~tq~~p~~--g-ssg~~~l~~~~f~m~I~qT~TG 77 (134)
T COG5122 1 MAVEQFFIINKSGGLIFQREFGEGETELNSNEYLILASTLHGVSAILTQTIPLP--G-SSGRLVLYFRNFVMTIFQTTTG 77 (134)
T ss_pred CceeEEEEEecCCcEEEEEeccCCccccCcccEEEEeechhhhhhhhhhcccCC--C-CCceEEEEeccEEEEEEEecCC
Confidence 567899999999999999999654332 1 0 111111111100 1 122 4444543 357788889
Q ss_pred EEEEEEe-cCCccHHHHHHHHHHHHHHHHhhc
Q psy918 162 LFIVSTT-KKNANIALVFVFLNKIVRVFTEYF 192 (504)
Q Consensus 162 ly~v~~~-~~~~n~l~~~~~L~~i~~vl~~y~ 192 (504)
+-||+++ +...|.++- |+.+.....+|.
T Consensus 78 ~kFV~~~~k~t~na~~q---l~kiY~lYsdYV 106 (134)
T COG5122 78 TKFVFVAEKRTVNALFQ---LQKIYSLYSDYV 106 (134)
T ss_pred cEEEEEecCCchhHHHH---HHHHHHHHHHHh
Confidence 9999998 444455433 677777777777
No 26
>KOG0997|consensus
Probab=68.31 E-value=36 Score=36.45 Aligned_cols=71 Identities=18% Similarity=0.412 Sum_probs=49.3
Q ss_pred eeEEEeCCCCeeeeeecccCcc---hhHHHHHHHHhhcccccCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCccHH
Q psy918 102 ALYILDVKGKVLISRNYRGDVE---MGVIEKFMPLLMEKEEEGMLTPLLQTSDCTFAYIKYNNLFIVSTTKKNANIA 175 (504)
Q Consensus 102 ~~~i~~~~G~vl~~r~y~~~~~---~~~~~~f~~~v~~~~~~~~~~pv~~~~~~~~v~~~~~~ly~v~~~~~~~n~l 175 (504)
-+||++.-|+.+.+|+-..+.- -++..+...-+... +..-..+..+|.++++..++-|++||+++.+..+.
T Consensus 119 hifilseaGKPiyS~~gs~e~l~stmGv~~alISf~q~~---~~~i~si~a~g~k~vfl~kspl~LvA~s~t~~Sa~ 192 (523)
T KOG0997|consen 119 HIFILSEAGKPIYSRHGSDEALSSTMGVMQALISFFQVS---GLAITSIHAFGNKLVFLQKSPLLLVAVSRTSQSAA 192 (523)
T ss_pred eEEEEecCCCceeeecCcHHHHHHHHHHHHHHHHHHhhC---CceEEEEEecCceEEEEecCcEEEEEEcccccCHH
Confidence 3799999999999987554322 23444433322211 23335678899999999999999999998776654
No 27
>KOG0781|consensus
Probab=63.08 E-value=65 Score=34.80 Aligned_cols=113 Identities=23% Similarity=0.257 Sum_probs=69.8
Q ss_pred heeeeEEEeCCCCeeeeeecccCcchhHHHHHHHHhhcccccCCCCCEEEeCCEEEEEEEeC--CEEEEEEecCCccHHH
Q psy918 99 SASALYILDVKGKVLISRNYRGDVEMGVIEKFMPLLMEKEEEGMLTPLLQTSDCTFAYIKYN--NLFIVSTTKKNANIAL 176 (504)
Q Consensus 99 ~i~~~~i~~~~G~vl~~r~y~~~~~~~~~~~f~~~v~~~~~~~~~~pv~~~~~~~~v~~~~~--~ly~v~~~~~~~n~l~ 176 (504)
|++.+.|+++.|.+|-...=.++.-+.-...|.+.++.....+... +..+.++.=|...+ ++.|+++-..-.+-..
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 5788999999999998744334333444566666544332111222 44555554555554 5677777655555556
Q ss_pred HHHHHHHHHHHHHhhcccccHHHHHhhHHHH-HHHHHH
Q psy918 177 VFVFLNKIVRVFTEYFKEIEEESIRDNFVVI-YELLDE 213 (504)
Q Consensus 177 ~~~~L~~i~~vl~~y~~~l~e~~i~~n~~~i-~~lldE 213 (504)
+-.+|....+...+-+...+-..++.|++.. .++|++
T Consensus 79 v~~ll~~v~~~f~e~~~~~~~~~l~~n~~~~~~e~lk~ 116 (587)
T KOG0781|consen 79 VDKLLNDVLNLFREKYDTQSALSLLNNTFDFQEELLKL 116 (587)
T ss_pred HHHHHHHHHHHHHHHhccchHHHhhhhhHHHHHHHHHH
Confidence 6678888888888777776677788887544 444443
No 28
>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=61.75 E-value=1.2e+02 Score=27.16 Aligned_cols=92 Identities=14% Similarity=0.196 Sum_probs=55.5
Q ss_pred eeeeEEEeCCCCeeeeeecccCc----ch---h----------HHHHHHHHhhcccccC---CCC--CEEEeCCEEE-EE
Q psy918 100 ASALYILDVKGKVLISRNYRGDV----EM---G----------VIEKFMPLLMEKEEEG---MLT--PLLQTSDCTF-AY 156 (504)
Q Consensus 100 i~~~~i~~~~G~vl~~r~y~~~~----~~---~----------~~~~f~~~v~~~~~~~---~~~--pv~~~~~~~~-v~ 156 (504)
|..++|+|+.|..+..|.|.... ++ + .+.+|..++.-.+... ... ..++++..+. +|
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 45789999999999999998643 11 1 1445555544311100 011 2455666654 66
Q ss_pred EEeCCEEEEEEecCCccHHHHHHHHHHHHHHHHhhc
Q psy918 157 IKYNNLFIVSTTKKNANIALVFVFLNKIVRVFTEYF 192 (504)
Q Consensus 157 ~~~~~ly~v~~~~~~~n~l~~~~~L~~i~~vl~~y~ 192 (504)
...-++-||++++.+...+ .-.+++.+.++.-+|.
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 7788999999999988543 4447888888888887
No 29
>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=52.51 E-value=1.4e+02 Score=26.71 Aligned_cols=72 Identities=22% Similarity=0.297 Sum_probs=35.9
Q ss_pred heeeeEEEeCCCCeeeeeeccc-CcchhHHHHHHHHhhccccc----CCCCCEEE-------eCCEEEEE-E-EeCCEEE
Q psy918 99 SASALYILDVKGKVLISRNYRG-DVEMGVIEKFMPLLMEKEEE----GMLTPLLQ-------TSDCTFAY-I-KYNNLFI 164 (504)
Q Consensus 99 ~i~~~~i~~~~G~vl~~r~y~~-~~~~~~~~~f~~~v~~~~~~----~~~~pv~~-------~~~~~~v~-~-~~~~ly~ 164 (504)
|++.+.|++++|++|..-.=-| .....-+..|..++++.+.. ....-+.. .++..+.| + +.-.|||
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 5889999999999998632222 22234578888888875431 11122333 33566654 3 3347999
Q ss_pred EEEecC
Q psy918 165 VSTTKK 170 (504)
Q Consensus 165 v~~~~~ 170 (504)
|++-.+
T Consensus 81 VvTyae 86 (148)
T PF09201_consen 81 VVTYAE 86 (148)
T ss_dssp EEEESS
T ss_pred EEEecc
Confidence 988654
No 30
>KOG3369|consensus
Probab=41.76 E-value=2.4e+02 Score=26.21 Aligned_cols=45 Identities=16% Similarity=0.253 Sum_probs=34.7
Q ss_pred EEEeCCE-EEEEEEeCCEEEEEEecCCccHHHHHHHHHHHHHHHHhhc
Q psy918 146 LLQTSDC-TFAYIKYNNLFIVSTTKKNANIALVFVFLNKIVRVFTEYF 192 (504)
Q Consensus 146 v~~~~~~-~~v~~~~~~ly~v~~~~~~~n~l~~~~~L~~i~~vl~~y~ 192 (504)
+++.+.. -++|+..-++=||++++.-. ..+-.+|+++.++..||.
T Consensus 125 ~LetdtF~l~~~QTlTG~KFVvis~~~~--~~aD~lLrKiYelYsDyv 170 (199)
T KOG3369|consen 125 VLETDTFTLHIFQTLTGTKFVVIAEPGT--QGADSLLRKIYELYSDYV 170 (199)
T ss_pred EEEeccEEEEEEEccCCcEEEEEecCCc--hhHHHHHHHHHHHHHHHh
Confidence 5556644 46889999999999987665 334568999999999997
No 31
>KOG3368|consensus
Probab=35.98 E-value=2.5e+02 Score=24.91 Aligned_cols=90 Identities=23% Similarity=0.321 Sum_probs=51.5
Q ss_pred hheeeeEEEeCCCCeeeeeecccCcc----hh-----------HHHHHHHHhhcccccCCCCCEEE--eCCEEE-EEEEe
Q psy918 98 MSASALYILDVKGKVLISRNYRGDVE----MG-----------VIEKFMPLLMEKEEEGMLTPLLQ--TSDCTF-AYIKY 159 (504)
Q Consensus 98 v~i~~~~i~~~~G~vl~~r~y~~~~~----~~-----------~~~~f~~~v~~~~~~~~~~pv~~--~~~~~~-v~~~~ 159 (504)
|.|-.++|+|+.|..|..+.|..... +. .+..|..++...+. ...+.. +...+. .|-.-
T Consensus 1 Mtiy~~yIFdR~g~Cl~y~EW~r~~~s~~~~eee~KL~yGmlFSlkS~v~Kls~~d~---k~~f~sy~Ts~YklhfyeTp 77 (140)
T KOG3368|consen 1 MTIYNFYIFDRNGVCLFYREWNRTKQSGIPNEEEAKLMYGMLFSLKSFVSKLSPGDV---KDGFLSYKTSKYKLHFYETP 77 (140)
T ss_pred CeEEEEEEEcCCccEEEehhcccccccCCchhHHHHHHHHHHhhHHHHHHhcCCCCc---ccCeeEEeeceeEEEEEEcC
Confidence 56778899999999999998854322 11 13444444433221 122332 333333 22334
Q ss_pred CCEEEEEEecCCccHHHHHHHHHHHHH-HHHhhc
Q psy918 160 NNLFIVSTTKKNANIALVFVFLNKIVR-VFTEYF 192 (504)
Q Consensus 160 ~~ly~v~~~~~~~n~l~~~~~L~~i~~-vl~~y~ 192 (504)
.+|.||..|+..+.. +-+.||.|.. +--+|.
T Consensus 78 tglk~vl~Tdpk~~~--ir~vLq~IYs~lyVE~V 109 (140)
T KOG3368|consen 78 TGLKFVLNTDPKAGS--IRDVLQYIYSHLYVEYV 109 (140)
T ss_pred CCcEEEEecCCCccc--HHHHHHHHHHHHHHHHH
Confidence 689999998877544 3456677666 434443
No 32
>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=34.07 E-value=2.9e+02 Score=23.39 Aligned_cols=87 Identities=7% Similarity=0.067 Sum_probs=47.0
Q ss_pred eeeeEEEeCCCCeeeeeecccCcchhHHHHHHHHhhcccccCCCCCEEEeCCEEEEEE-------------------EeC
Q psy918 100 ASALYILDVKGKVLISRNYRGDVEMGVIEKFMPLLMEKEEEGMLTPLLQTSDCTFAYI-------------------KYN 160 (504)
Q Consensus 100 i~~~~i~~~~G~vl~~r~y~~~~~~~~~~~f~~~v~~~~~~~~~~pv~~~~~~~~v~~-------------------~~~ 160 (504)
+....|++.+|.+..+..--..+.......+.+.+.+... ....-+.++|.+|... +.+
T Consensus 16 ~~~aaI~~~dG~vwA~s~~f~~~~~~E~~~i~~~f~~~~~--~~~~gi~l~G~kY~~~~~d~~~i~~k~~~~G~~i~kt~ 93 (121)
T PF00235_consen 16 ITKAAIIGSDGSVWASSPGFSNISPEEAKAIIKAFNNPSK--FPSNGITLGGKKYIVLRADDNSIYGKKGKGGIIIVKTK 93 (121)
T ss_dssp ESEEEEEETTSSEEEEETTGGGCSHHHHHHHHHHHHSSSH--HHHH-EEETTEEEEEEEEETTEEEEEETTEEEEEEECS
T ss_pred EeEEEEEcCCCCEEEecCCCCCCCHHHHHHHHHHhcCchh--cccCCeEEcCcEeEEEecCCceEEeeCCCCcEEEEECC
Confidence 4556888999987776442112222233333332222110 1112344555554443 334
Q ss_pred CEEEEEEecCCccHHHHHHHHHHHHHHH
Q psy918 161 NLFIVSTTKKNANIALVFVFLNKIVRVF 188 (504)
Q Consensus 161 ~ly~v~~~~~~~n~l~~~~~L~~i~~vl 188 (504)
..++|++...+.++-.+.....++++.|
T Consensus 94 ~~ivIg~y~~~~~~~~~~~~v~~lA~yL 121 (121)
T PF00235_consen 94 QAIVIGMYDESIQPGNCNKAVEKLADYL 121 (121)
T ss_dssp SEEEEEEEETTSTHHHHHHHHHHHHHHH
T ss_pred CEEEEEEeCCCCCHHHHHHHHHHHHhhC
Confidence 5677777777778888888887777654
No 33
>PF13598 DUF4139: Domain of unknown function (DUF4139)
Probab=32.82 E-value=3.7e+02 Score=26.98 Aligned_cols=107 Identities=18% Similarity=0.401 Sum_probs=59.3
Q ss_pred CcCCCceEEEeCCCCceeEEEEEecCCCCCceEEEE----------EEEecccEEEEEEEEeeccCCCccccceEEEEec
Q psy918 342 RFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIES----------VIERFVHSRVEYMIKAKSQFKRRSTANNVEIVIP 411 (504)
Q Consensus 342 ~f~~~r~i~F~PPdG~F~Lm~Yr~~~~~~~P~~i~~----------~~~~~~~~~le~~l~l~~~~~~~~~~~~v~I~iP 411 (504)
.|-.+..|.+++|.++|.| .+-..... .+.. ++.+....+.++.+.++...+ ..-.|.|.=+
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-SFGVDPDV----RVERKLLKKEEERGFFGKSQRRTYEYTITVRNNKD---EPVTVTVEDQ 265 (317)
T ss_pred EEEEeeecCCCCCCCEEEE-EcccCCCE----EEEEEecceecccccccccEEEEEEEEEEEECCCC---CCEEEEEEeC
Confidence 4556678999999988884 34443221 1111 111111234556666664432 3346888878
Q ss_pred CCCCCCCCeEEeee---eEEEEeCCCcEEEEEeceecCCceEEEEEEEEe
Q psy918 412 VPADADSPKFKTTI---GSVKYTPEQSAITWTIKSFPGGKEYLMRAHFGL 458 (504)
Q Consensus 412 ~P~~~~~~~~~~s~---G~~~~~~~~~~lvW~I~k~~g~~~~~l~~~~~l 458 (504)
+|.... ..+.... .....+...+.+.|++ .++.+.+..++..+.+
T Consensus 266 iPvs~~-~~I~V~~~~~~~~~~~~~~g~~~W~~-~l~~g~~~~l~~~y~v 313 (317)
T PF13598_consen 266 IPVSED-EDIKVELLEPPEPNEDEKDGILEWKV-TLPPGESRTLEFSYEV 313 (317)
T ss_pred CCCCCC-ceEEEEEcCCCCCcccCCCCEEEEEE-EECCCCEEEEEEEEEE
Confidence 886542 2232211 1224568889999998 5655555556655544
No 34
>KOG1766|consensus
Probab=30.07 E-value=62 Score=26.82 Aligned_cols=43 Identities=21% Similarity=0.418 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHHhhcccc--cHHHHHhhHHHHHHHHHHHHhCC
Q psy918 176 LVFVFLNKIVRVFTEYFKEI--EEESIRDNFVVIYELLDELIDFG 218 (504)
Q Consensus 176 ~~~~~L~~i~~vl~~y~~~l--~e~~i~~n~~~i~~lldEiid~G 218 (504)
.+-+.|..++++.++++++. +-..|-.....+|+++|.+.|-.
T Consensus 24 sv~e~megiCk~yEe~Lkk~nPs~~~ITYDIsqlfeFiD~L~DlS 68 (104)
T KOG1766|consen 24 SVTECMEGICKMYEEHLKKKNPSAPPITYDISQLFEFIDDLADLS 68 (104)
T ss_pred hHHHHHHHHHHHHHHHHHhcCCCCCCcceeHHHHHHHHHHHhhhh
Confidence 46678999999999999754 66778888999999999998754
No 35
>KOG0862|consensus
Probab=25.90 E-value=2.3e+02 Score=27.22 Aligned_cols=48 Identities=15% Similarity=0.324 Sum_probs=41.9
Q ss_pred EEEeCCEEEEEEEeCCEEEEEEecCCccHHHHHHHHHHHHHHHHhhcc
Q psy918 146 LLQTSDCTFAYIKYNNLFIVSTTKKNANIALVFVFLNKIVRVFTEYFK 193 (504)
Q Consensus 146 v~~~~~~~~v~~~~~~ly~v~~~~~~~n~l~~~~~L~~i~~vl~~y~~ 193 (504)
-++.+...|-|+..+++.+.++++.+-+--+++.+|+.+.+=+..-++
T Consensus 53 Sietg~f~fHfli~~~Vcylvicd~~yP~kLAF~YLedL~~EF~~~~~ 100 (216)
T KOG0862|consen 53 SIETGPFVFHFLIESGVCYLVICDKSYPRKLAFSYLEDLAQEFDKSYG 100 (216)
T ss_pred ccccCCeEEEEEecCCEEEEEEecCCCcHHHHHHHHHHHHHHHHHhcc
Confidence 466777888999999999999999999999999999999988777665
No 36
>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=23.72 E-value=4e+02 Score=21.65 Aligned_cols=43 Identities=19% Similarity=0.377 Sum_probs=27.9
Q ss_pred ccceEEEEecCCCCCCCCeEEeeeeEEEEeCCCcEEEEEeceecCCc
Q psy918 402 TANNVEIVIPVPADADSPKFKTTIGSVKYTPEQSAITWTIKSFPGGK 448 (504)
Q Consensus 402 ~~~~v~I~iP~P~~~~~~~~~~s~G~~~~~~~~~~lvW~I~k~~g~~ 448 (504)
-+-||.|+=.+|-+. ++-.+.-.++ -...+.++|+|+++-.+.
T Consensus 43 DcvnVviTqqLPce~---eFV~SdPett-p~~D~kLVW~Ig~l~~G~ 85 (95)
T PF03504_consen 43 DCVNVVITQQLPCEV---EFVRSDPETT-PTPDGKLVWKIGRLGQGE 85 (95)
T ss_pred ceeEEEEeecCCcce---EEEecCCccc-cCCCCEEEEEeccccCCc
Confidence 467899998888864 2322322222 234578999999997554
Done!