Query 018279
Match_columns 358
No_of_seqs 122 out of 974
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 07:39:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018279.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018279hhsearch_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 9.8E-94 2.1E-98 648.5 31.4 353 1-356 65-446 (446)
2 KOG0937 Adaptor complexes medi 100.0 1.2E-82 2.6E-87 601.0 33.8 357 1-357 66-424 (424)
3 KOG2740 Clathrin-associated pr 100.0 6E-70 1.3E-74 498.1 29.0 336 1-357 68-418 (418)
4 PF00928 Adap_comp_sub: Adapto 100.0 1.8E-61 3.9E-66 449.7 31.1 261 89-357 1-262 (262)
5 KOG2635 Medium subunit of clat 100.0 1.7E-34 3.8E-39 270.7 26.8 324 1-355 67-511 (512)
6 KOG2677 Stoned B synaptic vesi 100.0 2.2E-35 4.8E-40 286.3 8.2 253 97-356 583-890 (922)
7 PF01217 Clat_adaptor_s: Clath 99.4 4.9E-13 1.1E-17 112.8 7.4 71 1-71 68-138 (141)
8 PF10291 muHD: Muniscin C-term 99.2 9.3E-09 2E-13 95.1 23.8 227 103-355 3-256 (257)
9 COG5030 APS2 Clathrin adaptor 97.6 0.00013 2.9E-09 59.5 5.1 64 2-65 69-132 (152)
10 KOG0934 Clathrin adaptor compl 97.5 7.3E-05 1.6E-09 60.9 3.1 59 4-62 71-129 (145)
11 KOG0935 Clathrin adaptor compl 97.3 0.00018 3.9E-09 57.2 3.4 62 5-66 73-134 (143)
12 KOG3343 Vesicle coat complex C 96.5 0.0056 1.2E-07 51.3 5.4 71 4-74 78-149 (175)
13 KOG0936 Clathrin adaptor compl 96.4 0.012 2.6E-07 48.9 7.1 71 2-72 75-145 (182)
14 COG5541 RET3 Vesicle coat comp 87.1 0.74 1.6E-05 38.7 3.5 71 4-74 85-156 (187)
15 PF15001 AP-5_subunit_s1: AP-5 77.5 9.8 0.00021 33.5 7.0 66 2-67 118-184 (189)
16 PF13598 DUF4139: Domain of un 47.2 1.5E+02 0.0032 28.0 9.4 112 179-295 194-313 (317)
17 PF08460 SH3_5: Bacterial SH3 46.6 83 0.0018 22.5 5.8 34 313-353 27-60 (65)
18 PF03504 Chlam_OMP6: Chlamydia 39.6 1.7E+02 0.0036 22.2 7.9 43 239-285 43-85 (95)
19 KOG0647 mRNA export protein (c 28.5 1.9E+02 0.0041 27.5 6.5 110 110-229 203-313 (347)
20 TIGR01451 B_ant_repeat conserv 28.3 1.5E+02 0.0032 20.1 4.5 31 221-253 11-41 (53)
21 PRK09750 hypothetical protein; 28.0 48 0.001 23.2 1.9 15 333-347 10-24 (64)
22 PF08784 RPA_C: Replication pr 26.7 1.1E+02 0.0023 23.7 4.0 22 39-60 78-99 (102)
23 PF07151 DUF1391: Protein of u 25.3 76 0.0017 20.8 2.3 16 188-203 16-31 (49)
24 PRK06764 hypothetical protein; 23.2 1.9E+02 0.0041 22.0 4.4 47 307-357 40-90 (105)
No 1
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=9.8e-94 Score=648.55 Aligned_cols=353 Identities=44% Similarity=0.783 Sum_probs=325.2
Q ss_pred CeeecCCCChHHHHHHHHHHHHHHHHHhhccchHHHHhcHHHHHHHHHHHhcCCeeeecChHHHHHhhcccccccccc--
Q 018279 1 MTASRQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDAYRMEVT-- 78 (358)
Q Consensus 1 v~vt~~~~n~~~~l~~L~~~~~~l~~y~~~l~e~~I~~n~~~i~elldE~id~G~p~~t~~~~Lk~~i~~~s~~~~~~-- 78 (358)
|++|++|.|.+.++|||.++.+++..|||.++|+.|++||.+|||+||||+||||||+|+++.|+.+|..++...+-.
T Consensus 65 vaitksN~Nva~v~eFl~kl~avm~aYfgk~~Eeaiknnf~lI~ElLDemld~G~pqnte~~al~~~is~~~Vrs~g~~l 144 (446)
T KOG0938|consen 65 VAITKSNANVAAVFEFLYKLDAVMNAYFGKDREEAIKNNFVLIYELLDEMLDFGIPQNTEPNALKAQISQKGVRSMGGVL 144 (446)
T ss_pred EEEecCCCchhhHHHHHHHHHHHHHHHhcccchhhhhhceEeHHHHHHHHHhcCCCccCChhHHHhhhhhhhhhcccccc
Confidence 689999999999999999999999999999999999999999999999999999999999999999998887655421
Q ss_pred -------CCCC----CccccccccccCCcccccceEEEEEEEeEEEEEeccCcEEEEEEEEEEEEEEEecCCCeEEEEec
Q 018279 79 -------QRPP----MAVTNAVSWRSEGIQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLN 147 (358)
Q Consensus 79 -------~~~~----~~~~~~~~wr~~~~~~~~neI~vdV~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln 147 (358)
++++ ++.++.++||+.|++|++||+|+||.|.+|.+++++|++++++|.|.|.|+++|||||+|+++||
T Consensus 145 s~k~s~~sq~~~~~ssqv~G~i~WRr~Gi~ykknevfldvvErvNlLmS~~GnVLrs~VsG~V~mk~~LSGmPeckfGlN 224 (446)
T KOG0938|consen 145 SSKSSPTSQATELRSSQVTGKIGWRREGIKYKKNEVFLDVVERVNLLMSSDGNVLRSDVSGTVDMKTHLSGMPECKFGLN 224 (446)
T ss_pred CCcCCCCcccccccccccccccccccccceeccceeEeEehheeeeEEcCCCCEEEeecccEEEEEEeccCCcccccccC
Confidence 1111 34467899999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhh-hcCC-------C-----CCCceeeeccceeeeeeccccccCCceEEEeCCCCeEEEEEEEecCCC-CCcEEEE
Q 018279 148 DRILLE-AQGR-------S-----TKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLNTQV-KPLIWVE 213 (358)
Q Consensus 148 ~~~~~~-~~~~-------~-----~~~~~~~l~d~~fH~cV~~~~~~~~~~i~F~PPdG~f~Ll~Y~~~~~~-~P~~~v~ 213 (358)
|...++ .++. . +....+.|+||+||+||++++|+++++|+|+||||+|+||+||+..++ +|| .+.
T Consensus 225 Dkl~~e~kq~esks~~~n~~~~sks~~g~v~leDc~FHqCV~L~kFn~eh~IsFvPPDGe~ELMkYr~~enInlPF-rV~ 303 (446)
T KOG0938|consen 225 DKLGMESKQSESKSDFGNKNFPSKSGKGSVLLEDCTFHQCVRLDKFNSEHIISFVPPDGEFELMKYRVTENINLPF-RVT 303 (446)
T ss_pred cccceeeccccccccccccCCCcccCCceEEeeccchheeeccccccccceEEEeCCCCceEeEeeeeccCcccce-Eee
Confidence 998876 2221 1 244668999999999999999999999999999999999999999887 777 467
Q ss_pred EEEEEccceEEEEEEEeeecCCCcceeeeEEEEecCCCCCCCceEEecceeEEEeCCCcEEEEEecccCCCceeEEEEEE
Q 018279 214 AQVERHSRSRVEILVKARSQFKERSTATNVEIELPVSSDASNPDVRTSMGSASYVPEDEALIWKIRSFPGGKEYMLRAEF 293 (358)
Q Consensus 214 ~~~~~~~~~~~e~~l~~~~~~~~~~~~~~v~i~iP~P~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~~~~~~~~~l~~~~ 293 (358)
|.++..+.+++||++.+++.|+++..+.+|.++||+|+++..+.++++.|+|+|.+++++++|+|+++.|.+|.+|++++
T Consensus 304 PiV~el~r~kie~ri~iks~f~~kl~a~~v~~rIPvP~ntv~~n~~v~~Gkaky~psen~ivWki~kf~G~tE~tlsAev 383 (446)
T KOG0938|consen 304 PIVTELGRTKIEYRITIKSLFPPKLLAKDVVVRIPVPPNTVKCNISVSNGKAKYVPSENAIVWKINKFNGLTESTLSAEV 383 (446)
T ss_pred eheecccceeEEEEEEEeccCCchhhhcceEEEecCCCccccceeEEecCccccCcccceEEEEecccCCcccceeEEEE
Confidence 99998888999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecCCC-CCCCCCCCCCceEEEEEECccccccceEEEEEEee-cCCCccccceEEEEEeCcEEEE
Q 018279 294 TLPSIT-AEEATPERKAPIRVKFEIPYFTVSGIQVRYLKIIE-KSGYHALPWVRYITMAGEYELR 356 (358)
Q Consensus 294 ~~~~~~-~~~~~~~~~~pi~v~F~i~~~s~SGl~V~~l~v~~-~~~~~~~k~vrY~t~sg~Y~~r 356 (358)
++.+.. +...| ..+||+|+|++|||+.|||.|++++|.+ +++|+..|||||+|+||+||+|
T Consensus 384 els~Tt~nkq~W--trPPIsleFeV~MFt~SGL~VrylkV~e~~Sk~~~vkWVrYitkaGsyEiR 446 (446)
T KOG0938|consen 384 ELSDTTQNKQQW--TRPPISLEFEVPMFTNSGLVVRYLKVSEKDSKHRAVKWVRYITKAGSYEIR 446 (446)
T ss_pred EeccCccccccc--cCCCceeEEeeeeecCCceEEEEEEEecccCCCceEEEEEEecccceeeeC
Confidence 998765 45578 8999999999999999999999999999 5899999999999999999998
No 2
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.2e-82 Score=600.97 Aligned_cols=357 Identities=62% Similarity=1.054 Sum_probs=331.0
Q ss_pred CeeecCCCChHHHHHHHHHHHHHHHHHhhccchHHHHhcHHHHHHHHHHHhcCCeeeecChHHHHHhhcccccccccc-C
Q 018279 1 MTASRQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDAYRMEVT-Q 79 (358)
Q Consensus 1 v~vt~~~~n~~~~l~~L~~~~~~l~~y~~~l~e~~I~~n~~~i~elldE~id~G~p~~t~~~~Lk~~i~~~s~~~~~~-~ 79 (358)
|++++.|++++.+++||+++++++.+||+.|.|+.+++||.++||+|||+|||||||.|+...|++|+.++++..... .
T Consensus 66 v~~~~~n~~a~~v~~~l~~~~~v~~~y~~~l~e~si~~n~vlvyElLde~mDFGypQ~t~s~iL~~yi~~~~~~l~~~~~ 145 (424)
T KOG0937|consen 66 VAGTRPNVSAALVLSFLYAVADVFGDYLSELEEESIRDNFVLVYELLDEVMDFGYPQTTDSEILKNYITQKANRLQDAQP 145 (424)
T ss_pred EEEeccCCCHHHHHHHHHHHHHHHHHHhccCCccceecchHHHHHHHHHHhccCCcccchHHHHHHHhcccccceeecCC
Confidence 467889999999999999999999999999999999999999999999999999999999999999999997765532 2
Q ss_pred CCCCccccccccccCCcccccceEEEEEEEeEEEEEeccCcEEEEEEEEEEEEEEEecCCCeEEEEeccchhhhhcCCCC
Q 018279 80 RPPMAVTNAVSWRSEGIQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQGRST 159 (358)
Q Consensus 80 ~~~~~~~~~~~wr~~~~~~~~neI~vdV~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~~~~ 159 (358)
++|.+.+++++||+.+++|+|||+|+||+|+++++++++|.++.++|.|+|.|||+|+|||+++|+||+....+.++..+
T Consensus 146 ~~p~avtnavsWrs~gi~~~KnevflDViE~Vs~l~~~~G~vl~s~i~G~I~~k~~LsGmPelrl~ln~~~~~~~~~~~~ 225 (424)
T KOG0937|consen 146 RPPLAVTNAVSWRSEGIYYGKNEVFLDVIESVSLLYDSNGIVLLSEIVGTIKLKCYLSGMPELRLGLNDKVLFDKQGPRS 225 (424)
T ss_pred CCCcccccceeecccccccccceEEEEhhhhhhHhhhcCCcEEEeeeeeEEEEEEEcCCCceeeeecCcccccccccccc
Confidence 56888899999999999999999999999999999999999999999999999999999999999999998876665334
Q ss_pred CCceeeeccceeeeeeccccccCCceEEEeCCCCeEEEEEEEecCCCCCcEEEEEEEEEccceEEEEEEEeeecCCCcce
Q 018279 160 KGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLNTQVKPLIWVEAQVERHSRSRVEILVKARSQFKERST 239 (358)
Q Consensus 160 ~~~~~~l~d~~fH~cV~~~~~~~~~~i~F~PPdG~f~Ll~Y~~~~~~~P~~~v~~~~~~~~~~~~e~~l~~~~~~~~~~~ 239 (358)
++..+.++|++||+||++++|+.+|+|+|+||||+|+||+||++..+.|++++....+.++..++++.++++++|+.+..
T Consensus 226 ~s~~v~ledi~fh~~v~l~~fd~dr~i~FiPPdGeF~Lm~Y~ls~~vkPli~~~~~~~~~~~~ri~i~~K~~~~fk~~~~ 305 (424)
T KOG0937|consen 226 KSKGVELEDIKFHECVRLSRFDNDRTISFIPPDGEFELMRYRLSTHVKPLIWFYQLIEEHSRSRIEVMVKLREQFKSRSS 305 (424)
T ss_pred cCcceEeeecccceeechhhccCCceEEecCCCCceEEEEEEecCCCCCeEEeeeeeeeccceeEEEEEechhhcCCccc
Confidence 45788999999999999999999999999999999999999999999999988655556677899999999999999999
Q ss_pred eeeEEEEecCCCCCCCceEEecceeEEEeCCCcEEEEEecccCCCceeEEEEEEEecCCCCCCCCCCCCCceEEEEEECc
Q 018279 240 ATNVEIELPVSSDASNPDVRTSMGSASYVPEDEALIWKIRSFPGGKEYMLRAEFTLPSITAEEATPERKAPIRVKFEIPY 319 (358)
Q Consensus 240 ~~~v~i~iP~P~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~pi~v~F~i~~ 319 (358)
+.+|.|+||+|..++.+++..+.|+++|.+++++++|+|++++|+.+.++++++.+++...++.-....+||+|+|+||+
T Consensus 306 a~~v~I~iP~P~~a~~~~fk~s~G~~~~~~e~~~l~W~I~~~~gg~e~~~r~~~~lp~~~~e~~~~~~~~pi~v~FeIp~ 385 (424)
T KOG0937|consen 306 ANNVEICIPVPDDASSPSFKTSLGSAKYDPEKSALRWTIKKFVGGKEYSLRARMDLPSEEHEEQCTEGLGPIKVKFEIPY 385 (424)
T ss_pred cceEEEEeeCCCccccceEeccCCceeeecccceEEEEeccccCCceEEEEEeecCCccccCCCCcccCCceEEEEEecc
Confidence 99999999999999999999999999999999999999999999999999999999886554411138899999999999
Q ss_pred cccccceEEEEEEee-cCCCccccceEEEEEeCcEEEEe
Q 018279 320 FTVSGIQVRYLKIIE-KSGYHALPWVRYITMAGEYELRL 357 (358)
Q Consensus 320 ~s~SGl~V~~l~v~~-~~~~~~~k~vrY~t~sg~Y~~r~ 357 (358)
+|.||++|+++++.+ +.+|++.+||||.|+||.|++|+
T Consensus 386 ~T~SgiqVrylki~ep~~~y~s~~WVRy~T~s~~Y~~r~ 424 (424)
T KOG0937|consen 386 FTVSGIQVRYLKIIEPKSQYQSLPWVRYNTQSGPYEIRV 424 (424)
T ss_pred cccCCeEEEEEEecccccCCCccceEEEEccCCceEeeC
Confidence 999999999999999 78999999999999999999994
No 3
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=6e-70 Score=498.10 Aligned_cols=336 Identities=32% Similarity=0.587 Sum_probs=296.5
Q ss_pred CeeecCCCChHHHHHHHHHHHHHHHHHhhccchHHHHhcHHHHHHHHHHHhcCCeeeecChHHHHHhhccccccccc---
Q 018279 1 MTASRQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDAYRMEV--- 77 (358)
Q Consensus 1 v~vt~~~~n~~~~l~~L~~~~~~l~~y~~~l~e~~I~~n~~~i~elldE~id~G~p~~t~~~~Lk~~i~~~s~~~~~--- 77 (358)
|+++..++.|+++++||||+++++++|||+++|.+|++|+..||||||||+|+|+|..||+|.||++|+.++...+.
T Consensus 68 ~~~st~e~pPL~~iefL~rv~dv~~eyFg~~s~~~Ik~N~~vv~ell~emiDnGfpl~tE~NiLke~i~pps~l~~~~~s 147 (418)
T KOG2740|consen 68 CAVSTVETPPLMVIEFLHRVVDVLLEYFGGLSESKIKDNVVVVYELLDEMIDNGFPLVTEPNILKELIPPPSFLSKKFNS 147 (418)
T ss_pred EEEEeccCCChhHHHHHHHHHHHHHHHhcccCHhHhhcceeeHHHHHHHHHHcCCCcccChhHHHhhcCChHHHHHHHhh
Confidence 47788899999999999999999999999999999999999999999999999999999999999999999887632
Q ss_pred -------cCCCCCccccccccccCCcccccceEEEEEEEeEEEEEeccCcEEEEEEEEEEEEEEEecCCCeEEEEeccch
Q 018279 78 -------TQRPPMAVTNAVSWRSEGIQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRI 150 (358)
Q Consensus 78 -------~~~~~~~~~~~~~wr~~~~~~~~neI~vdV~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~ 150 (358)
+.+.|..+...+|||+.+.+|.+||.||||.|+++|+++++|..+.++|.|.|.|+|+|+|||++.|.|+++.
T Consensus 148 vTg~~n~~~~lPtg~~s~VPWR~~~~Ky~nNE~yvdvlEeidai~~k~gslv~~eI~g~vd~~~qLsgmPdltlsl~np~ 227 (418)
T KOG2740|consen 148 VTGNSNVSDTLPTGALSNVPWRTAGVKYTNNEAYVDVLEEIDAIVDKKGSLVFGEIQGIVDVCSQLSGMPDLTLSLNNPR 227 (418)
T ss_pred hhccccccccCCCcccccccccccCcccccchhhhhhhheeheEecCCCCEEEEEEEEEEEEEEeecCCCceEEEccCcc
Confidence 2245666677799999999999999999999999999999999999999999999999999999999998864
Q ss_pred hhhhcCCCCCCceeeeccceeeeeeccccccCCceEEEeCCCCeEEEEEEEecCC--C-CCcEEEEEEEEEccce--EEE
Q 018279 151 LLEAQGRSTKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLNTQ--V-KPLIWVEAQVERHSRS--RVE 225 (358)
Q Consensus 151 ~~~~~~~~~~~~~~~l~d~~fH~cV~~~~~~~~~~i~F~PPdG~f~Ll~Y~~~~~--~-~P~~~v~~~~~~~~~~--~~e 225 (358)
.|+|++|||||+..+|++++.|+|+||||+|+||+||++.+ . +|- .+.++++..+.. +++
T Consensus 228 --------------~L~dvsfHpcVr~krwe~~~~lsFIPPDGkFrLlsy~v~~~~~v~~pv-yv~~~i~l~~~~~~ri~ 292 (418)
T KOG2740|consen 228 --------------LLGDVSFHPCVRYKRWESHSVLSFIPPDGKFRLLSYRVDAQNQVAIPV-YVKNSISLDSNHQGRIS 292 (418)
T ss_pred --------------ccCCcccccceeecccccccceEEcCCCCcEEEEEEEEehhhccccce-EEeeeeccCCCceEEEE
Confidence 48999999999999999999999999999999999999764 3 555 467777655443 444
Q ss_pred EEEEeeecCCCcceeeeEEEEecCCCCCCCceEEecceeEEEeCCCcEEEEEecccCCCceeEEEEEEEecCCCCCCCCC
Q 018279 226 ILVKARSQFKERSTATNVEIELPVSSDASNPDVRTSMGSASYVPEDEALIWKIRSFPGGKEYMLRAEFTLPSITAEEATP 305 (358)
Q Consensus 226 ~~l~~~~~~~~~~~~~~v~i~iP~P~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~~~~~~~~~l~~~~~~~~~~~~~~~~ 305 (358)
+.+..+...++ ..+.+.|+...|+.........++|+..++...+.+-|+++++..+.-+.|++++.+.+... ...
T Consensus 293 ~tvg~~~~~gK--~ie~itVt~~~pn~i~~~~k~~~~g~~~~~~~~k~l~W~~~~i~tg~lp~Lkg~~~~e~~~s-k~~- 368 (418)
T KOG2740|consen 293 LTVGPKKKMGK--TIELITVTVQDPNEIAYASKILTHGTFTNSIIMKQLTWTFGSIATGKLPVLKGTINLEPGFS-KKV- 368 (418)
T ss_pred Eeccccccccc--eeEeEEEEecCccceeeeecccccceeEeecccceeEEEeecccCCcccccccccccCCCCC-ccc-
Confidence 44444444333 45778899999999988888889999999999999999999999888889999998875422 233
Q ss_pred CCCCceEEEEEECccccccceEEEEEEeecCCCccccceEEEEEeCcEEEEe
Q 018279 306 ERKAPIRVKFEIPYFTVSGIQVRYLKIIEKSGYHALPWVRYITMAGEYELRL 357 (358)
Q Consensus 306 ~~~~pi~v~F~i~~~s~SGl~V~~l~v~~~~~~~~~k~vrY~t~sg~Y~~r~ 357 (358)
.++.++++|++.+.++||++|+.+++.+ ..|+||||+||.|+||.+++|+
T Consensus 369 -~l~t~~Lqykiqg~alsglkVe~Ldm~~-~~~k~yKGvKy~t~agnfqvR~ 418 (418)
T KOG2740|consen 369 -DLPTLSLQYKIQGQALSGLKVERLDMYG-EPYKPYKGVKYKTKAGNFQVRL 418 (418)
T ss_pred -cCcccceeeeeeeeeccceEEEeeeecC-CCCccccceEEEEeeeeEEEeC
Confidence 7889999999999999999999999997 5788999999999999999995
No 4
>PF00928 Adap_comp_sub: Adaptor complexes medium subunit family; InterPro: IPR008968 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. This entry represents the C-terminal domain of the mu subunit from various clathrin adaptors (AP1, AP2 and AP3) []. The C-teminal domain has an immunoglobulin-like beta-sandwich fold consisting of 9 strands in 2 sheets with a Greek key topology, similar to that found in cytochrome f and certain transcription factors []. The mu subunit regulates the coupling of clathrin lattices with particular membrane proteins by self-phosphorylation via a mechanism that is still unclear []. The mu subunit possesses a highly conserved N-terminal domain of around 230 amino acids, which may be the region of interaction with other AP proteins; a linker region of between 10 and 42 amino acids; and a less well-conserved C-terminal domain of around 190 amino acids, which may be the site of specific interaction with the protein being transported in the vesicle []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 1H6E_A 3L81_A 1W63_V 4EMZ_A 4EN2_A 2VGL_M 3ML6_F 2PR9_A 2JKT_M 1I31_A ....
Probab=100.00 E-value=1.8e-61 Score=449.67 Aligned_cols=261 Identities=40% Similarity=0.787 Sum_probs=217.6
Q ss_pred cccccCCcccccceEEEEEEEeEEEEEeccCcEEEEEEEEEEEEEEEecCCCeEEEEeccchhhhhcCCCCCCceeeecc
Q 018279 89 VSWRSEGIQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQGRSTKGKAIDLDD 168 (358)
Q Consensus 89 ~~wr~~~~~~~~neI~vdV~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~l~d 168 (358)
+|||+.+++|++|||||||.|+|+|+++++|.++.++|.|+|.|+|+|+|+|+|+|+||++... ...++.++|
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 5899999999999999999999999999999999999999999999999999999999987422 134568999
Q ss_pred ceeeeeeccccccCCceEEEeCCCCeEEEEEEEecCCCCCcEEEEEEEEEccceEEEEEEEeeecCCCcceeeeEEEEec
Q 018279 169 IKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLNTQVKPLIWVEAQVERHSRSRVEILVKARSQFKERSTATNVEIELP 248 (358)
Q Consensus 169 ~~fH~cV~~~~~~~~~~i~F~PPdG~f~Ll~Y~~~~~~~P~~~v~~~~~~~~~~~~e~~l~~~~~~~~~~~~~~v~i~iP 248 (358)
++|||||++++|++++.|+|+||||+|+||+||++....+|+.+.|++...+++++++.++++++++....+++|.|+||
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 99999999999999999999999999999999998877666678899888667899999999999988788999999999
Q ss_pred CCCCCCCceEEecceeEEEeCCCcEEEEEecccCCCceeEEEEEEEecCCCCCCCCCCCCCceEEEEEECccccccceEE
Q 018279 249 VSSDASNPDVRTSMGSASYVPEDEALIWKIRSFPGGKEYMLRAEFTLPSITAEEATPERKAPIRVKFEIPYFTVSGIQVR 328 (358)
Q Consensus 249 ~P~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~pi~v~F~i~~~s~SGl~V~ 328 (358)
+|+++..+++..+.|+++|+.+++.++|+|++++++.+++++|++++......+. ...++||.|+|++|++++||++|+
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 9999889999999999999999999999999999999999999999976544332 126889999999999999999999
Q ss_pred EEEEee-cCCCccccceEEEEEeCcEEEEe
Q 018279 329 YLKIIE-KSGYHALPWVRYITMAGEYELRL 357 (358)
Q Consensus 329 ~l~v~~-~~~~~~~k~vrY~t~sg~Y~~r~ 357 (358)
+++|.+ ..+|+|+|||||.|+||+||||+
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 999998 36899999999999999999995
No 5
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.7e-34 Score=270.70 Aligned_cols=324 Identities=17% Similarity=0.277 Sum_probs=250.8
Q ss_pred CeeecCCCChHHHHHHHHHHHHHHHHHhhccchHHHHhcHHHHHHHHHHHhcCCeeeecChHHHHHhhcccccccccc--
Q 018279 1 MTASRQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDAYRMEVT-- 78 (358)
Q Consensus 1 v~vt~~~~n~~~~l~~L~~~~~~l~~y~~~l~e~~I~~n~~~i~elldE~id~G~p~~t~~~~Lk~~i~~~s~~~~~~-- 78 (358)
|++|++++|++.++++|+.|.+++.+||..|+|..|..|.+.+...|||++..||..+.++.|+|+|..|+||++++.
T Consensus 67 vLITtk~SNIleDl~TL~Lfskvipey~~slde~eI~~~~FelifAFDEivsLGyre~v~laQikty~eMdSHEEKi~e~ 146 (512)
T KOG2635|consen 67 VLITTKQSNILEDLETLRLFSKVIPEYCSSLDEKEILENAFELIFAFDEIVSLGYRENVNLAQIKTYLEMDSHEEKIHEL 146 (512)
T ss_pred EEEeccccchhhHHHHHHHHHHhchhhhhhhhHHHHHHhhhhhhhccchhhhhcccccccHHHhhhhhccccHHHHHHHH
Confidence 579999999999999999999999999999999999999999999999999999999999999999999999998850
Q ss_pred --------------------------------C-----------------------------CCC----Cccccccc---
Q 018279 79 --------------------------------Q-----------------------------RPP----MAVTNAVS--- 90 (358)
Q Consensus 79 --------------------------------~-----------------------------~~~----~~~~~~~~--- 90 (358)
+ +.+ .+...+.|
T Consensus 147 v~~nke~ea~q~mkrKaKElqr~r~ea~rrgg~~~~~~~~~~s~g~~~~s~~~~~~~~~~~~~~~~~~sa~~~~s~pak~ 226 (512)
T KOG2635|consen 147 VMRNKEREAKQEMKRKAKELQRARKEAERRGGSLNPGFDAIGSSGYSSVSTTNAINRVESIAQKPKQQSAAKASSAPAKA 226 (512)
T ss_pred HHHhhhHHHHHHHHHHHHHHHHHHHhhhccccccCCCccccccccccCCcccchhhccccccccccccccccCCCCCchh
Confidence 0 000 00000000
Q ss_pred --------------------------------cc------cCCcccccceEEEEEEEeEEEEEeccCcEEEEEEEEEEEE
Q 018279 91 --------------------------------WR------SEGIQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKM 132 (358)
Q Consensus 91 --------------------------------wr------~~~~~~~~neI~vdV~E~i~~~~~~~G~i~~~~v~G~i~~ 132 (358)
.+ +......++.|++.+.|+|++.+++||.+.+.++.|.+.+
T Consensus 227 mklG~k~~~s~~~~d~Lk~ege~ia~~~s~~g~~s~aap~~~~p~v~~e~v~i~ieEkln~~~~RDGgi~s~E~qG~lsL 306 (512)
T KOG2635|consen 227 MKLGKKTKNSDTFVDKLKGEGERIAGASSAIGSASSAAPPPTAPDVPEESVHIVIEEKLNVRLSRDGGIKSGEVQGTLSL 306 (512)
T ss_pred hhhcccccchhhHHHHhhccccccccccccccccccCCCCCCCCCCccceEEEEEeeeEeEEEcccCCccceeeeeeEEE
Confidence 00 0011223455999999999999999999999999999999
Q ss_pred EEEecCCCeEEEEeccchhhhhcCCCCCCceeeeccceeeeeeccccccCCceEEEeCCCCeEE------EEEEEecC--
Q 018279 133 RTYLSGMPECKLGLNDRILLEAQGRSTKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFD------LMTYRLNT-- 204 (358)
Q Consensus 133 ~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~l~d~~fH~cV~~~~~~~~~~i~F~PPdG~f~------Ll~Y~~~~-- 204 (358)
+..-....++.|.|++... .+ .++++||++|++.|.++..|.+++|+..|+ ||+||...
T Consensus 307 rI~d~e~~~i~lkl~n~~~----------~g---~q~ktHPNlDK~~f~s~s~iglk~~~K~FPvn~~VGvLkWR~~~~d 373 (512)
T KOG2635|consen 307 RIKDEEYGDIELKLANGRD----------KG---TQLKTHPNLDKKVFLSSSLIGLKRPEKPFPVNSDVGVLKWRMVDED 373 (512)
T ss_pred EEccccccceEEEEcCCCC----------cc---eeeeeCCCcchhhhccccccccccCCCCCCcCCcceEEEEeecccc
Confidence 9988888888988976321 22 368999999999999999999999999997 79999965
Q ss_pred -CCCCcEEEEEEEEEccce---EEEEEEEeeecCCCcceeeeEEEEecCCCCCCCceEEecceeEEEeCCCcEEEEEecc
Q 018279 205 -QVKPLIWVEAQVERHSRS---RVEILVKARSQFKERSTATNVEIELPVSSDASNPDVRTSMGSASYVPEDEALIWKIRS 280 (358)
Q Consensus 205 -~~~P~~~v~~~~~~~~~~---~~e~~l~~~~~~~~~~~~~~v~i~iP~P~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~ 280 (358)
...|+ .++||.+..+.+ .+||++...+ ..+||.|.||+|.++ .+++....|.+.|+..++.+.|.|+.
T Consensus 374 es~iPl-TincWPSes~~g~dV~iEYe~~~~~------eL~dV~i~iPlP~~i-apsv~~~Dge~~~~~~~~~leW~I~~ 445 (512)
T KOG2635|consen 374 ESEIPL-TINCWPSESGNGYDVNIEYEAVLEC------ELNDVIITIPLPANI-APSVGECDGEYRYDERKNVLEWSIGV 445 (512)
T ss_pred cccCce-EEEeccccCCCCeEEEEEEeehhcc------cccceEEEeeccccc-CCccceecceEEeccccceeEEEeee
Confidence 34777 578998876543 4666663322 467999999999988 88899999999999999999999999
Q ss_pred cCCCceeEEEEEEEecCCCCCCCCCCCCCceEEEEEECccccccceEEEEEEeecCCCcccc-ceEEEEEeCcEEE
Q 018279 281 FPGGKEYMLRAEFTLPSITAEEATPERKAPIRVKFEIPYFTVSGIQVRYLKIIEKSGYHALP-WVRYITMAGEYEL 355 (358)
Q Consensus 281 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~pi~v~F~i~~~s~SGl~V~~l~v~~~~~~~~~k-~vrY~t~sg~Y~~ 355 (358)
+..+. +|.++|.-.. ..++ .++|++|.|... .+++|+.|..+.-.. +..|.+ -++=.-.+..|++
T Consensus 446 Ia~N~----SGslEFs~~~-~~~~--~fFPl~VsF~s~-~~ftgl~vqkVv~~~--~~~~~~y~~~t~f~~dky~V 511 (512)
T KOG2635|consen 446 IAKNF----SGSLEFSCPA-SDPD--GFFPLSVSFTSD-TVFTGLFVQKVVRND--GHAPVRYSVETTFEVDKYEV 511 (512)
T ss_pred eccCC----CCcEEEeecC-CCCC--ceeeEEEEEEec-ccccceEEEEEEEcC--CCCCceeEEEEEEEeeeeEe
Confidence 94332 3444443111 1344 899999999987 699999999775543 223322 2333333466765
No 6
>KOG2677 consensus Stoned B synaptic vesicle biogenesis protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.2e-35 Score=286.34 Aligned_cols=253 Identities=28% Similarity=0.505 Sum_probs=212.0
Q ss_pred ccccceEEEEEEEeEEEEEeccCcEEEEEEEEEEEEEEEecCCCeEEEEeccchhhhhcC--C-C----CCCceeeeccc
Q 018279 97 QYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQG--R-S----TKGKAIDLDDI 169 (358)
Q Consensus 97 ~~~~neI~vdV~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~--~-~----~~~~~~~l~d~ 169 (358)
.|..+||.|||.+..++.++++|.++...|..+|.|.|||+|+|+|.|+|||..+.+... + + ....||.|.+|
T Consensus 583 nY~e~EI~v~~~Defsg~V~Keg~~~~~~v~tri~cL~FlsG~~ec~lgLND~~~kg~Eiv~rkDimp~~t~kwI~~~~~ 662 (922)
T KOG2677|consen 583 NYLEEEITVDVRDEFSGIVSKEGQILQHHVLTRIHCLSFLSGLAECRLGLNDILVKGNEIVLRKDIMPTTTTKWIKLHEC 662 (922)
T ss_pred ccccceeEEEEEeccceeecccchhhhhhhhhhhhhhhhccCCceeEeecchhhhcccceeEeccccccccccceeeeee
Confidence 588999999999999999999999999999999999999999999999999987533210 1 1 35689999999
Q ss_pred eeeeeeccccccCCceEEEeCCCC-eEEEEEEEecCC--CCCcEEEEEEEEEccceEEEEEEEee--ecC------CCcc
Q 018279 170 KFHQCVRLARFENDRTISFIPPDG-SFDLMTYRLNTQ--VKPLIWVEAQVERHSRSRVEILVKAR--SQF------KERS 238 (358)
Q Consensus 170 ~fH~cV~~~~~~~~~~i~F~PPdG-~f~Ll~Y~~~~~--~~P~~~v~~~~~~~~~~~~e~~l~~~--~~~------~~~~ 238 (358)
.||.|||.+.|+++|+|.|.|||| .|+|||||+..+ .+|+. +...+.. .+.++|+..-++ +.| ...+
T Consensus 663 ~FH~cVn~~eF~~srVI~F~PlDaCrFElMRFrt~~~~~~lpft-lks~~~V-~Ga~VEvq~~~~mat~~qr~rd~~~~v 740 (922)
T KOG2677|consen 663 RFHGCVNEDEFHNSRVILFNPLDACRFELMRFRTVFAEKTLPFT-LKSATSV-NGAEVEVQSWLRMATGFQRNRDPLTQV 740 (922)
T ss_pred eeecccchhhccccceEEecCcccceeeeeeeeeecCCCcCcee-eeeeeee-ccceeehHHHHHHHhhhhhccCccccC
Confidence 999999999999999999999999 999999999653 58885 4444433 567788764332 222 2346
Q ss_pred eeeeEEEEecCCCCC--------------------------------CCceEEecceeEEEeCCCcEEEEEecccCCCc-
Q 018279 239 TATNVEIELPVSSDA--------------------------------SNPDVRTSMGSASYVPEDEALIWKIRSFPGGK- 285 (358)
Q Consensus 239 ~~~~v~i~iP~P~~~--------------------------------~~~~~~~~~G~~~~~~~~~~l~W~I~~~~~~~- 285 (358)
.|+|+.|++|+|..| +.+.++++.|+++|+...+.|+|+|++++.++
T Consensus 741 pCenI~IrfPVPs~WIk~fr~e~~~g~kSlkaK~nR~a~~gsl~~~~sepvi~vt~G~AKYEhay~siVWrI~RLPdKns 820 (922)
T KOG2677|consen 741 PCENIMIRFPVPSEWIKNFRRESVLGEKSLKAKVNRGASFGSLSVSGSEPVIRVTLGTAKYEHAYNSIVWRINRLPDKNS 820 (922)
T ss_pred cccceeEeccCcHHHHHHHHHHhhhccchhhhhhcccccccchhhccCCceEEEeecchhhHHhhhhheeecccCCcccc
Confidence 799999999999864 12467889999999999999999999998644
Q ss_pred ----eeEEEEEEEecCCCCCCCCCCCCCceEEEEEECccccccceEEEEEEeecCCCccccceEEEEEeCcEEEE
Q 018279 286 ----EYMLRAEFTLPSITAEEATPERKAPIRVKFEIPYFTVSGIQVRYLKIIEKSGYHALPWVRYITMAGEYELR 356 (358)
Q Consensus 286 ----~~~l~~~~~~~~~~~~~~~~~~~~pi~v~F~i~~~s~SGl~V~~l~v~~~~~~~~~k~vrY~t~sg~Y~~r 356 (358)
+|-|.|.++|.++++.+.+ ..+.+.|+|.+|..++|...||++.|.. ...+.|||+|..+ .+|++-
T Consensus 821 a~~hpHcl~c~lELgSd~evPs~--f~p~~~V~FsmP~t~aS~t~VRSisVE~--~~~v~K~V~y~A~-Y~yqv~ 890 (922)
T KOG2677|consen 821 ASGHPHCLFCHLELGSDREVPSR--FAPHVNVEFSMPTTSASKTSVRSISVED--KTDVRKWVNYSAH-YSYQVA 890 (922)
T ss_pred ccCCCeeEEEEEeccccccCchh--hccccceeeeccccccccceeeeeeccc--cccHHHHHhhhhh-eeeeee
Confidence 6889999999998877666 7889999999999999999999999986 4458999999876 667654
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=99.41 E-value=4.9e-13 Score=112.76 Aligned_cols=71 Identities=34% Similarity=0.571 Sum_probs=64.6
Q ss_pred CeeecCCCChHHHHHHHHHHHHHHHHHhhccchHHHHhcHHHHHHHHHHHhcCCeeeecChHHHHHhhccc
Q 018279 1 MTASRQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTD 71 (358)
Q Consensus 1 v~vt~~~~n~~~~l~~L~~~~~~l~~y~~~l~e~~I~~n~~~i~elldE~id~G~p~~t~~~~Lk~~i~~~ 71 (358)
+++++.+.|+++++++|+++.++|++||+.++|..|+.||+.+|++||||+|+|+|+.||++.+...+.+.
T Consensus 68 ~~v~~~~eNel~~~e~l~~~v~~l~~~~~~v~e~~i~~N~~~v~~~LDEiid~G~i~etd~~~I~~~v~~~ 138 (141)
T PF01217_consen 68 VVVGDENENELLLLEFLHRLVEVLDDYFGNVSEKDILENFDLVYLILDEIIDGGIILETDPNVILKRVTMQ 138 (141)
T ss_dssp EEEESSTSBHHHHHHHHHHHHHHHHHHHSS-SHHHHHHTHHHHHHHHHHHEETTEES--THHHHHHHHHHC
T ss_pred EEEeecccchHHHHHHHHHhhhhhhhhhccccHHHHHHCHHHHHHHHHHHHhCCEEEECCHHHHHHHHHHh
Confidence 47889999999999999999999999999999999999999999999999999999999999998888654
No 8
>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=99.20 E-value=9.3e-09 Score=95.08 Aligned_cols=227 Identities=19% Similarity=0.281 Sum_probs=121.7
Q ss_pred EEEEEEEeEEEEEeccCcEEEEEEEEEEEEEEEecC------CCeEEEEeccchhhhhcCCCCCCceeeeccceeeeeec
Q 018279 103 VFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSG------MPECKLGLNDRILLEAQGRSTKGKAIDLDDIKFHQCVR 176 (358)
Q Consensus 103 I~vdV~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG------~P~~~l~ln~~~~~~~~~~~~~~~~~~l~d~~fH~cV~ 176 (358)
+-..|.|+|||.+. +|.+....|.|+|.+.---.- .+.+.++|++... |+.+.-.+..=
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 LNASITETVNAYFK-GGQLSKVKVTGEVALSYPAGISSSLTSPPPLSFRLNNFSR--------------LEKIAPNPQFV 67 (257)
T ss_dssp EEEEEEEEEEEEEE-TTEEEEEEEEEEEEEEEE--SSS-----SEEEEEEETGGG--------------EEEEEE-TTTE
T ss_pred eeEEEEEEEEEEEE-CCcEEEEEEEEEEEEecCCChhhcccCCCcEEEEEcCcch--------------hceeecCHhHe
Confidence 55679999999998 788999999999998743322 3456788876543 22222211110
Q ss_pred cccccCCceEEEeCCC--CeE--EEEEEEecC-----CCCCcEEEEEEEEEc-cceEEEEEEEeee-cCCCcceeeeEEE
Q 018279 177 LARFENDRTISFIPPD--GSF--DLMTYRLNT-----QVKPLIWVEAQVERH-SRSRVEILVKARS-QFKERSTATNVEI 245 (358)
Q Consensus 177 ~~~~~~~~~i~F~PPd--G~f--~Ll~Y~~~~-----~~~P~~~v~~~~~~~-~~~~~e~~l~~~~-~~~~~~~~~~v~i 245 (358)
...-.++....|.++. ... ..|+|++.. ...|++ +.+.-+.. ....+-+.++... .+......+||.|
T Consensus 68 ~~~~~~~~~f~~n~~~l~~~~~~~alKYqv~~~~~~~~~~Pl~-l~~~Wk~e~~~tsl~l~Y~~Np~~~~~~~~L~nv~~ 146 (257)
T PF10291_consen 68 SSSSQSDGEFWLNMSALTSHLPKQALKYQVHSDPSNLSSVPLI-LKPVWKCEPSQTSLILDYKLNPDAFASPVPLENVVF 146 (257)
T ss_dssp --EEEETTEEEE-TTTTBT-E-EEEEEEEEES--------SEE-EEEEEEE-SSEEEEEEEEEE-TTT--E-EEEEEEEE
T ss_pred ecCCCCCCcEEEehHHhhhhhhhceEEEEEeccccccCCCCeE-EEeEEEeCCceEEEEEEEEeChhhccccceeeeEEE
Confidence 0011123345555553 333 579999976 446665 44433332 2233444444444 4444567899999
Q ss_pred EecCCCC-CCCceEEecceeEEEeCCCcEEEEEecccC--CCce-eEEEEEEEecCCCCCCCCCCCCCceEEEEEEC-cc
Q 018279 246 ELPVSSD-ASNPDVRTSMGSASYVPEDEALIWKIRSFP--GGKE-YMLRAEFTLPSITAEEATPERKAPIRVKFEIP-YF 320 (358)
Q Consensus 246 ~iP~P~~-~~~~~~~~~~G~~~~~~~~~~l~W~I~~~~--~~~~-~~l~~~~~~~~~~~~~~~~~~~~pi~v~F~i~-~~ 320 (358)
.+++... +.++.. .-.+.|..+++.+.|+++.+. ++.+ ..|.|.+..... .. ...+|.++|++. +.
T Consensus 147 ~v~l~g~~~ts~~s---kP~g~~~~e~~ri~Wrl~el~~~~~~~~~kL~ARf~~~~~----~~--~p~~v~vkF~~~~~~ 217 (257)
T PF10291_consen 147 SVPLDGGRATSAQS---KPQGTWNKEKNRITWRLPELSLTSEGEGGKLIARFMTSGG----PS--RPGGVEVKFEIEGGS 217 (257)
T ss_dssp EEEB-SS-EEEEEE---SSS--B-SSS-EEEEE-SSEEEETT---EEEEEEEEESS----------SS-EEEEEEE---S
T ss_pred EEEcCCcccccccc---CCCccccCCCcEEEEECCcccccCCCCCceEEEEEECCCC----CC--CCceEEEEEEEcCCC
Confidence 9999876 333333 334678899999999999765 3333 688999876542 22 567899999999 88
Q ss_pred ccccceEEEEEEeec-----CCCccccceEEEEEeCcEEE
Q 018279 321 TVSGIQVRYLKIIEK-----SGYHALPWVRYITMAGEYEL 355 (358)
Q Consensus 321 s~SGl~V~~l~v~~~-----~~~~~~k~vrY~t~sg~Y~~ 355 (358)
+.||+.|.-..-.+. .+|+. -=++-...||.|..
T Consensus 218 ~~sg~~i~~~~~~~~~dp~~~~w~~-~~~~r~~~sGkY~~ 256 (257)
T PF10291_consen 218 TLSGLGISLVYQDDEEDPPGGGWRL-VLVKRKLVSGKYIA 256 (257)
T ss_dssp -SS----EEEEEESSS-TT----EE--EEEEEEEEEEEE-
T ss_pred cccCcEEEEeecccccCCCCCcceE-EEEEEEEeeeEEec
Confidence 899998887722211 12322 25677778899974
No 9
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=97.56 E-value=0.00013 Score=59.54 Aligned_cols=64 Identities=27% Similarity=0.333 Sum_probs=58.3
Q ss_pred eeecCCCChHHHHHHHHHHHHHHHHHhhccchHHHHhcHHHHHHHHHHHhcCCeeeecChHHHH
Q 018279 2 TASRQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILS 65 (358)
Q Consensus 2 ~vt~~~~n~~~~l~~L~~~~~~l~~y~~~l~e~~I~~n~~~i~elldE~id~G~p~~t~~~~Lk 65 (358)
++...+.|-+.+|+++|.|.+++..|||...|-.+--||..+|.+||||+-.|-.+.++++.+-
T Consensus 69 f~Vd~~dnEl~iL~lIh~FVE~lDr~FgnVCELdlIFNF~kv~~ILdE~i~gG~i~Es~~~~vl 132 (152)
T COG5030 69 FGVDNDDNELIILELIHNFVEILDRFFGNVCELDLIFNFQKVYAILDEMILGGEIIESSKNEVL 132 (152)
T ss_pred EEEcCCCCcchHHHHHHHHHHHHHHHhccceeeEeEeeHHHHHHHHHHHHhCCeeeecCHHHHH
Confidence 3455567899999999999999999999999999999999999999999999999999988654
No 10
>KOG0934 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.52 E-value=7.3e-05 Score=60.94 Aligned_cols=59 Identities=32% Similarity=0.411 Sum_probs=53.6
Q ss_pred ecCCCChHHHHHHHHHHHHHHHHHhhccchHHHHhcHHHHHHHHHHHhcCCeeeecChH
Q 018279 4 SRQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEAN 62 (358)
Q Consensus 4 t~~~~n~~~~l~~L~~~~~~l~~y~~~l~e~~I~~n~~~i~elldE~id~G~p~~t~~~ 62 (358)
...+.|-+.++|++|++.++|..|||+..|-.|.-||..+|.+|||++-.|-.|.+..+
T Consensus 71 v~~~dNEL~~LE~IH~~vE~lDkYFg~VCELDiiFNfekay~ILde~~~~g~~~e~~k~ 129 (145)
T KOG0934|consen 71 VEDNDNELAILEFIHNYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEIQETSKN 129 (145)
T ss_pred EecCCchhhHHHHHHHHHHHHHHHhccceeeEEEEehHhHHHHHHHHhcCcchHhhhcc
Confidence 34789999999999999999999999999999999999999999999998876666554
No 11
>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.35 E-value=0.00018 Score=57.16 Aligned_cols=62 Identities=29% Similarity=0.351 Sum_probs=55.7
Q ss_pred cCCCChHHHHHHHHHHHHHHHHHhhccchHHHHhcHHHHHHHHHHHhcCCeeeecChHHHHH
Q 018279 5 RQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSE 66 (358)
Q Consensus 5 ~~~~n~~~~l~~L~~~~~~l~~y~~~l~e~~I~~n~~~i~elldE~id~G~p~~t~~~~Lk~ 66 (358)
....|-+..++.+|.|.++|.+||+...|-.+.-||--+|.++|||+=.|-.+.|+...+-+
T Consensus 73 d~tDnelayLe~IHlFVEvLd~fF~NVCELDlvFNFyKVy~i~DEm~l~GEi~Etsk~~vle 134 (143)
T KOG0935|consen 73 DVTDNELAYLEHIHLFVEVLDEFFHNVCELDLVFNFYKVYTIVDEMFLAGEIRETSKTKVLE 134 (143)
T ss_pred ecCCchHHHHHHHHHHHHHHHHHhccccceeeeeeeeeHHHHHHHHHHhhhhhhhhHHHHHH
Confidence 45567888999999999999999999999999999999999999999999999998765433
No 12
>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=96.49 E-value=0.0056 Score=51.32 Aligned_cols=71 Identities=20% Similarity=0.293 Sum_probs=61.4
Q ss_pred ecCCCChHHHHHHHHHHHHHHHHHhhc-cchHHHHhcHHHHHHHHHHHhcCCeeeecChHHHHHhhcccccc
Q 018279 4 SRQNCNAASLLFFLHRVVDVFKHYFEE-LEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDAYR 74 (358)
Q Consensus 4 t~~~~n~~~~l~~L~~~~~~l~~y~~~-l~e~~I~~n~~~i~elldE~id~G~p~~t~~~~Lk~~i~~~s~~ 74 (358)
-..+-|-++..+.|+.|-+.+.-.++. ..-..+.+|++.|...+||++|.|....||++++-.-+...+..
T Consensus 78 G~~~ENEl~L~svL~~l~dal~llLr~nveKr~llEN~D~i~L~~DEiiD~GvILEtdp~~ia~rv~~~~~~ 149 (175)
T KOG3343|consen 78 GSEEENELMLMSVLTCLFDALSLLLRKNVEKRELLENLDLIFLALDEIIDGGVILETDPNQIAQRVALRPTD 149 (175)
T ss_pred cCcchhHHHHHHHHHHHHHHHHHHHHhChhHHHHHhhhccceeehhhhccCceEEecCHHHHHHHhccCCCC
Confidence 345778899999999999999988887 66677999999999999999999999999999998887766543
No 13
>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=96.45 E-value=0.012 Score=48.90 Aligned_cols=71 Identities=18% Similarity=0.179 Sum_probs=63.4
Q ss_pred eeecCCCChHHHHHHHHHHHHHHHHHhhccchHHHHhcHHHHHHHHHHHhcCCeeeecChHHHHHhhcccc
Q 018279 2 TASRQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDA 72 (358)
Q Consensus 2 ~vt~~~~n~~~~l~~L~~~~~~l~~y~~~l~e~~I~~n~~~i~elldE~id~G~p~~t~~~~Lk~~i~~~s 72 (358)
.+.+..-+-+.+|++++-|.+.|...|....|-.+.-|+..++-+|+|+.-.|....|+.+-+-.-+....
T Consensus 75 fvvD~sEsEL~iLDLIQvfVEtLDkCF~nVcELDliF~~~k~h~iL~EiV~GGmVlETn~neIv~av~~~n 145 (182)
T KOG0936|consen 75 FVVDSSESELGILDLIQVFVETLDKCFENVCELDLIFNWQKVHAILAEIVMGGMVLETNMNEIVAAVDEQN 145 (182)
T ss_pred EEEcCCcchhHHHHHHHHHHHHHHHHHHhhhhhhheeeHHHHHHHHHHHHhCCeEEeccHHHHHHHHHHhc
Confidence 45667778899999999999999999999999999999999999999999999999999998776665543
No 14
>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=87.08 E-value=0.74 Score=38.68 Aligned_cols=71 Identities=14% Similarity=0.138 Sum_probs=59.0
Q ss_pred ecCCCChHHHHHHHHHHHHHHHHHhhcc-chHHHHhcHHHHHHHHHHHhcCCeeeecChHHHHHhhcccccc
Q 018279 4 SRQNCNAASLLFFLHRVVDVFKHYFEEL-EEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDAYR 74 (358)
Q Consensus 4 t~~~~n~~~~l~~L~~~~~~l~~y~~~l-~e~~I~~n~~~i~elldE~id~G~p~~t~~~~Lk~~i~~~s~~ 74 (358)
..-+.|-.+.-+-+..|...|.-.++.. ++..+.+||+.|..+.||.||.|....|+++.+-+-++.++..
T Consensus 85 ~~meeNE~~l~q~f~~ir~Al~li~k~~~dkr~v~enYDqivl~vdEtid~Gvilet~s~~ia~rv~K~p~~ 156 (187)
T COG5541 85 SPMEENEPFLGQVFDEIRAALILIVKTPTDKRNVWENYDQIVLLVDETIDEGVILETKSDEIADRVPKPPNF 156 (187)
T ss_pred cccccccHHHHHHHHHHHHHHHHHHcCCcchhhHHhhhceEEEeeehhcccceEeecChHHHHHhCCCCCCc
Confidence 3446677788888899999888888874 5555999999999999999999999999999988888765443
No 15
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=77.51 E-value=9.8 Score=33.46 Aligned_cols=66 Identities=8% Similarity=0.057 Sum_probs=55.9
Q ss_pred eeecCCCChHHHHHHHHHHHHHHHHHhhccch-HHHHhcHHHHHHHHHHHhcCCeeeecChHHHHHh
Q 018279 2 TASRQNCNAASLLFFLHRVVDVFKHYFEELEE-ESLRDNFVVVYELLDEMMDFGYPQYTEANILSEF 67 (358)
Q Consensus 2 ~vt~~~~n~~~~l~~L~~~~~~l~~y~~~l~e-~~I~~n~~~i~elldE~id~G~p~~t~~~~Lk~~ 67 (358)
+|+...-|.+++-.||+.|...|.+.+..++. ..+....+.|.-+|+..++.|.-.-.+-+.+|.+
T Consensus 118 LVce~hEN~lLa~~~L~~~~~~l~~~~~~l~~~~e~l~k~d~i~aiL~~fLP~GQLLFlN~~~~k~l 184 (189)
T PF15001_consen 118 LVCEPHENRLLAENTLRLFIRHLLEHLKILSQPSEVLLKSDRILAILHRFLPHGQLLFLNHRFVKQL 184 (189)
T ss_pred EEecCchhHHHHHHHHHHHHHHHHHHHHHhCcHHHhhhhHHHHHHHHHHhCCCCcEEEEcHHHHHHH
Confidence 67889999999999999999999999987644 6677789999999999999998777666655543
No 16
>PF13598 DUF4139: Domain of unknown function (DUF4139)
Probab=47.17 E-value=1.5e+02 Score=27.96 Aligned_cols=112 Identities=19% Similarity=0.304 Sum_probs=56.1
Q ss_pred cccCCceEEEeCCCCeEEEEEEEecCCC----CCcE-EE-EEEEEEccceEEEEEEEeeecCCCcceeeeEEEEecCCCC
Q 018279 179 RFENDRTISFIPPDGSFDLMTYRLNTQV----KPLI-WV-EAQVERHSRSRVEILVKARSQFKERSTATNVEIELPVSSD 252 (358)
Q Consensus 179 ~~~~~~~i~F~PPdG~f~Ll~Y~~~~~~----~P~~-~v-~~~~~~~~~~~~e~~l~~~~~~~~~~~~~~v~i~iP~P~~ 252 (358)
.|-.+..|.+.+|.++|.| .+-.+..+ .+.. .. ...+......+.++++.++...+. .-.|.|.=++|-.
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 TFVGESRLPHTAPGEEFEL-SFGVDPDVRVERKLLKKEEERGFFGKSQRRTYEYTITVRNNKDE---PVTVTVEDQIPVS 269 (317)
T ss_pred EEEEeeecCCCCCCCEEEE-EcccCCCEEEEEEecceecccccccccEEEEEEEEEEEECCCCC---CEEEEEEeCCCCC
Confidence 3445567888899888874 34443321 0000 00 001111111245566666644332 2347777677653
Q ss_pred C-CCceEEecc-eeEEEeCCCcEEEEEecccCCCceeEEEEEEEe
Q 018279 253 A-SNPDVRTSM-GSASYVPEDEALIWKIRSFPGGKEYMLRAEFTL 295 (358)
Q Consensus 253 ~-~~~~~~~~~-G~~~~~~~~~~l~W~I~~~~~~~~~~l~~~~~~ 295 (358)
. ..+++.... .....+...+.+.|++.-=+| ...+++..+.+
T Consensus 270 ~~~~I~V~~~~~~~~~~~~~~g~~~W~~~l~~g-~~~~l~~~y~v 313 (317)
T PF13598_consen 270 EDEDIKVELLEPPEPNEDEKDGILEWKVTLPPG-ESRTLEFSYEV 313 (317)
T ss_pred CCceEEEEEcCCCCCcccCCCCEEEEEEEECCC-CEEEEEEEEEE
Confidence 3 223332221 122566789999999965444 44455555443
No 17
>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=46.62 E-value=83 Score=22.51 Aligned_cols=34 Identities=32% Similarity=0.670 Sum_probs=22.9
Q ss_pred EEEEECccccccceEEEEEEeecCCCccccceEEEEEeCcE
Q 018279 313 VKFEIPYFTVSGIQVRYLKIIEKSGYHALPWVRYITMAGEY 353 (358)
Q Consensus 313 v~F~i~~~s~SGl~V~~l~v~~~~~~~~~k~vrY~t~sg~Y 353 (358)
+-+..+ -|-.|.+-.+..+.+ +.|++|..-+|.+
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 18
>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=39.56 E-value=1.7e+02 Score=22.19 Aligned_cols=43 Identities=23% Similarity=0.364 Sum_probs=27.6
Q ss_pred eeeeEEEEecCCCCCCCceEEecceeEEEeCCCcEEEEEecccCCCc
Q 018279 239 TATNVEIELPVSSDASNPDVRTSMGSASYVPEDEALIWKIRSFPGGK 285 (358)
Q Consensus 239 ~~~~v~i~iP~P~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~~~~~~ 285 (358)
-+-||.|+-.+|-..+ +-.+...++ -...+.|+|+|+.+-.++
T Consensus 43 DcvnVviTqqLPce~e---FV~SdPett-p~~D~kLVW~Ig~l~~G~ 85 (95)
T PF03504_consen 43 DCVNVVITQQLPCEVE---FVRSDPETT-PTPDGKLVWKIGRLGQGE 85 (95)
T ss_pred ceeEEEEeecCCcceE---EEecCCccc-cCCCCEEEEEeccccCCc
Confidence 3668999999997643 222222222 135678999999987555
No 19
>KOG0647 consensus mRNA export protein (contains WD40 repeats) [RNA processing and modification]
Probab=28.49 E-value=1.9e+02 Score=27.54 Aligned_cols=110 Identities=17% Similarity=0.208 Sum_probs=68.8
Q ss_pred eEEEEEeccCcEEEEEEEEEEEEEEEecCCCeEEEEeccchhhhhcCCCCCCceeeeccceeeeeec-cccccCCceEEE
Q 018279 110 HVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQGRSTKGKAIDLDDIKFHQCVR-LARFENDRTISF 188 (358)
Q Consensus 110 ~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~l~d~~fH~cV~-~~~~~~~~~i~F 188 (358)
.|.|..|++|. ....|.|.+.+..--.++|.-.+.|.-...- +....+-.-+.++.|||--. +..-.+|.+.+|
T Consensus 203 ~va~f~d~~~~-alGsiEGrv~iq~id~~~~~~nFtFkCHR~~----~~~~~~VYaVNsi~FhP~hgtlvTaGsDGtf~F 277 (347)
T KOG0647|consen 203 CVACFQDKDGF-ALGSIEGRVAIQYIDDPNPKDNFTFKCHRST----NSVNDDVYAVNSIAFHPVHGTLVTAGSDGTFSF 277 (347)
T ss_pred EEEEEecCCce-EeeeecceEEEEecCCCCccCceeEEEeccC----CCCCCceEEecceEeecccceEEEecCCceEEE
Confidence 45666777877 6688999999998888888777777554211 00011233466799999322 334456788888
Q ss_pred eCCCCeEEEEEEEecCCCCCcEEEEEEEEEccceEEEEEEE
Q 018279 189 IPPDGSFDLMTYRLNTQVKPLIWVEAQVERHSRSRVEILVK 229 (358)
Q Consensus 189 ~PPdG~f~Ll~Y~~~~~~~P~~~v~~~~~~~~~~~~e~~l~ 229 (358)
-.-|.+-.|..|..-+ .|+ .+ |.+.. ++.-|-|-+.
T Consensus 278 WDkdar~kLk~s~~~~--qpI-tc-c~fn~-~G~ifaYA~g 313 (347)
T KOG0647|consen 278 WDKDARTKLKTSETHP--QPI-TC-CSFNR-NGSIFAYALG 313 (347)
T ss_pred ecchhhhhhhccCcCC--Ccc-ce-eEecC-CCCEEEEEee
Confidence 8888887788776432 333 32 55543 3445555554
No 20
>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=28.31 E-value=1.5e+02 Score=20.06 Aligned_cols=31 Identities=16% Similarity=0.125 Sum_probs=23.9
Q ss_pred ceEEEEEEEeeecCCCcceeeeEEEEecCCCCC
Q 018279 221 RSRVEILVKARSQFKERSTATNVEIELPVSSDA 253 (358)
Q Consensus 221 ~~~~e~~l~~~~~~~~~~~~~~v~i~iP~P~~~ 253 (358)
+..++|++.++...+ ..+.+|.|.=++|.+.
T Consensus 11 Gd~v~Yti~v~N~g~--~~a~~v~v~D~lP~g~ 41 (53)
T TIGR01451 11 GDTITYTITVTNNGN--VPATNVVVTDILPSGT 41 (53)
T ss_pred CCEEEEEEEEEECCC--CceEeEEEEEcCCCCC
Confidence 457899998876543 3478999999999874
No 21
>PRK09750 hypothetical protein; Provisional
Probab=27.95 E-value=48 Score=23.24 Aligned_cols=15 Identities=47% Similarity=0.807 Sum_probs=11.6
Q ss_pred eecCCCccccceEEE
Q 018279 333 IEKSGYHALPWVRYI 347 (358)
Q Consensus 333 ~~~~~~~~~k~vrY~ 347 (358)
.++.|-.|.+|+||.
T Consensus 10 i~KpGg~P~~W~r~s 24 (64)
T PRK09750 10 IEKEGGTPTNWTRYS 24 (64)
T ss_pred EECCCCCccceeEec
Confidence 345667799999995
No 22
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=26.66 E-value=1.1e+02 Score=23.65 Aligned_cols=22 Identities=23% Similarity=-0.043 Sum_probs=17.9
Q ss_pred cHHHHHHHHHHHhcCCeeeecC
Q 018279 39 NFVVVYELLDEMMDFGYPQYTE 60 (358)
Q Consensus 39 n~~~i~elldE~id~G~p~~t~ 60 (358)
+...|.++++++++-|+.+.|-
T Consensus 78 ~~~~v~~al~~L~~eG~IYsTi 99 (102)
T PF08784_consen 78 SENEVRKALDFLSNEGHIYSTI 99 (102)
T ss_dssp -HHHHHHHHHHHHHTTSEEESS
T ss_pred CHHHHHHHHHHHHhCCeEeccc
Confidence 3467889999999999988873
No 23
>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=25.30 E-value=76 Score=20.75 Aligned_cols=16 Identities=44% Similarity=0.731 Sum_probs=12.7
Q ss_pred EeCCCCeEEEEEEEec
Q 018279 188 FIPPDGSFDLMTYRLN 203 (358)
Q Consensus 188 F~PPdG~f~Ll~Y~~~ 203 (358)
|---||.|+.|.|.-+
T Consensus 16 fpn~dgtftamtytks 31 (49)
T PF07151_consen 16 FPNQDGTFTAMTYTKS 31 (49)
T ss_pred eeCCCCcEEEEEEeec
Confidence 4445899999999864
No 24
>PRK06764 hypothetical protein; Provisional
Probab=23.20 E-value=1.9e+02 Score=21.97 Aligned_cols=47 Identities=23% Similarity=0.418 Sum_probs=27.2
Q ss_pred CCCceEEEEEE-CccccccceEEEEEEeecCCCccccceEEE---EEeCcEEEEe
Q 018279 307 RKAPIRVKFEI-PYFTVSGIQVRYLKIIEKSGYHALPWVRYI---TMAGEYELRL 357 (358)
Q Consensus 307 ~~~pi~v~F~i-~~~s~SGl~V~~l~v~~~~~~~~~k~vrY~---t~sg~Y~~r~ 357 (358)
.+..|.+.... ..|.+||=.|+-+.= +.+...--||. .+-|.|.+|.
T Consensus 40 nfn~i~v~mn~~e~y~lsgrsidilsg----dkeaiqlnkyti~f~kpg~yvirv 90 (105)
T PRK06764 40 NFNAIDVSMNINELYVLSGRSIDVLSG----DKEAIQLNKYTIRFSKPGKYVIRV 90 (105)
T ss_pred ccceEEEEEeccceEEEcCceeeeecC----ChhheEeeeeEEEecCCccEEEEE
Confidence 45567776654 458899977765432 22233333343 3458888885
Done!