Query 017238
Match_columns 375
No_of_seqs 121 out of 1074
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 06:49:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017238.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017238hhsearch_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 3.4E-90 7.4E-95 630.8 35.5 367 6-374 43-446 (446)
2 KOG2740 Clathrin-associated pr 100.0 5.9E-80 1.3E-84 568.7 33.5 370 4-375 44-418 (418)
3 KOG0937 Adaptor complexes medi 100.0 1.4E-75 3E-80 558.0 36.0 360 4-375 42-424 (424)
4 PF00928 Adap_comp_sub: Adapto 100.0 9.8E-60 2.1E-64 442.1 30.3 247 127-375 1-262 (262)
5 KOG2635 Medium subunit of clat 100.0 1.6E-41 3.5E-46 320.7 31.6 356 8-373 47-511 (512)
6 KOG2677 Stoned B synaptic vesi 100.0 1.2E-34 2.7E-39 283.6 6.3 236 133-373 581-889 (922)
7 PF01217 Clat_adaptor_s: Clath 99.7 1.4E-17 3.1E-22 141.7 11.0 94 5-98 45-138 (141)
8 PF10291 muHD: Muniscin C-term 99.3 2.7E-09 5.9E-14 99.5 24.2 226 141-373 3-256 (257)
9 COG5030 APS2 Clathrin adaptor 99.0 1.8E-09 3.9E-14 88.2 7.3 86 8-93 48-133 (152)
10 KOG0934 Clathrin adaptor compl 98.9 7.9E-10 1.7E-14 90.2 4.1 85 5-89 45-129 (145)
11 KOG0935 Clathrin adaptor compl 98.7 2.4E-08 5.1E-13 79.6 6.5 80 13-92 54-133 (143)
12 KOG0936 Clathrin adaptor compl 98.4 6.5E-07 1.4E-11 74.4 6.7 90 13-102 59-148 (182)
13 KOG3343 Vesicle coat complex C 98.0 3E-05 6.4E-10 65.3 7.5 94 9-102 56-150 (175)
14 COG5541 RET3 Vesicle coat comp 96.6 0.0053 1.1E-07 51.7 6.2 93 8-100 62-155 (187)
15 PF15001 AP-5_subunit_s1: AP-5 92.9 0.52 1.1E-05 41.7 7.8 82 12-94 102-184 (189)
16 PF13774 Longin: Regulated-SNA 92.3 1 2.3E-05 34.1 8.0 48 9-56 18-65 (83)
17 PF03504 Chlam_OMP6: Chlamydia 77.1 15 0.00032 27.9 6.8 43 261-307 42-85 (95)
18 KOG0859 Synaptobrevin/VAMP-lik 76.5 22 0.00049 31.6 8.8 50 9-58 45-94 (217)
19 PF08923 MAPKK1_Int: Mitogen-a 57.3 70 0.0015 26.2 7.7 45 9-53 70-114 (119)
20 TIGR01451 B_ant_repeat conserv 51.9 51 0.0011 22.6 5.2 32 246-277 11-42 (53)
21 KOG0862 Synaptobrevin/VAMP-lik 49.8 64 0.0014 29.2 6.7 48 10-57 54-101 (216)
22 PRK06764 hypothetical protein; 49.5 56 0.0012 25.0 5.3 48 327-374 41-89 (105)
23 PF03164 Mon1: Trafficking pro 38.4 1.5E+02 0.0034 29.7 8.3 44 10-53 58-101 (415)
24 KOG0647 mRNA export protein (c 30.8 85 0.0018 30.1 4.6 104 146-256 201-315 (347)
25 PF01345 DUF11: Domain of unkn 24.5 1.8E+02 0.0039 21.1 4.7 32 246-277 40-71 (76)
26 PF10633 NPCBM_assoc: NPCBM-as 23.4 1.5E+02 0.0032 21.8 4.1 31 247-277 5-35 (78)
27 KOG1766 Enhancer of rudimentar 22.8 96 0.0021 24.2 2.9 42 40-81 25-68 (104)
28 PF02334 RTP: Replication term 20.1 1.7E+02 0.0036 23.7 3.8 34 47-83 37-70 (122)
No 1
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=3.4e-90 Score=630.82 Aligned_cols=367 Identities=29% Similarity=0.537 Sum_probs=332.9
Q ss_pred CCceEEeCCEEEEEEEeCCEEEEEEEcCCCChhhHHHHHHHHHHHHhhhcCCCCHHHHHhhHHHHHHHHHhHhhCCcccc
Q 017238 6 SMPVIASPTHYIFQIVRAGITFLACTQVEMPPLMGIEFLCRVADILSDYLGELNEDLIKDNFVIVYELLDEMIDNGFPLT 85 (375)
Q Consensus 6 ~~Pv~~~~~~~~~~~~~~~l~~v~v~~~~~n~~~~~~~L~~~~~vl~~y~~~l~e~~i~~n~~~i~~llde~id~G~p~~ 85 (375)
-+||.+.|++.|+|++.+++|+|++|..|.|.+++++||..+.+++..|||.++|+.|++||.+||||||||+||||||+
T Consensus 43 r~PV~~igsttf~~~r~~nl~lvaitksN~Nva~v~eFl~kl~avm~aYfgk~~Eeaiknnf~lI~ElLDemld~G~pqn 122 (446)
T KOG0938|consen 43 RSPVLTIGSTTFHHIRSSNLWLVAITKSNANVAAVFEFLYKLDAVMNAYFGKDREEAIKNNFVLIYELLDEMLDFGIPQN 122 (446)
T ss_pred CCCeeEecceeEEEEeeccEEEEEEecCCCchhhHHHHHHHHHHHHHHHhcccchhhhhhceEeHHHHHHHHHhcCCCcc
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cChHHHhhhcCCCcchhccc--ccccCCCCCccCCCCCCCCcCCcccCCCCCcccceEEEEEEEeEEEEEccCCcEEEEE
Q 017238 86 TEPNILREMIAPPNIVSKML--SVVTGNSSNVSDILPGATASCVPWRPTDVKYANNEVYVDLVEEMDAIINRDGVLVKCE 163 (375)
Q Consensus 86 t~~~~lk~~i~~~s~~~k~~--~~~~g~~~~~~~~~~~~~~~~~~WR~~~~~~~~nei~vdV~E~v~~~~~~~G~i~~~~ 163 (375)
|+++.|+.+|..+...++.- +......+++.....+.....++||+.|++|++||+|+||.|+++..++++|++++++
T Consensus 123 te~~al~~~is~~~Vrs~g~~ls~k~s~~sq~~~~~ssqv~G~i~WRr~Gi~ykknevfldvvErvNlLmS~~GnVLrs~ 202 (446)
T KOG0938|consen 123 TEPNALKAQISQKGVRSMGGVLSSKSSPTSQATELRSSQVTGKIGWRREGIKYKKNEVFLDVVERVNLLMSSDGNVLRSD 202 (446)
T ss_pred CChhHHHhhhhhhhhhccccccCCcCCCCcccccccccccccccccccccceeccceeEeEehheeeeEEcCCCCEEEee
Confidence 99999999999887755411 1000001111112223456789999999999999999999999999999999999999
Q ss_pred EEEEEEEEEeeCCCCeeEEEecCCc---------------------------ccccceecceeecCCCCCCceEEEeCCC
Q 017238 164 IYGEVQVNCLLSGLPDLTLSFANPS---------------------------ILHDVRFHPCVRFRPWESHQILSFVPPD 216 (375)
Q Consensus 164 v~G~i~~~~~LsG~P~~~l~ln~~~---------------------------~l~d~~fH~cV~~~~f~~~~~i~f~PPd 216 (375)
|.|.|.|+++|||||+|+++|||.. .++||+||+||++++|++++.|+|+|||
T Consensus 203 VsG~V~mk~~LSGmPeckfGlNDkl~~e~kq~esks~~~n~~~~sks~~g~v~leDc~FHqCV~L~kFn~eh~IsFvPPD 282 (446)
T KOG0938|consen 203 VSGTVDMKTHLSGMPECKFGLNDKLGMESKQSESKSDFGNKNFPSKSGKGSVLLEDCTFHQCVRLDKFNSEHIISFVPPD 282 (446)
T ss_pred cccEEEEEEeccCCcccccccCcccceeeccccccccccccCCCcccCCceEEeeccchheeeccccccccceEEEeCCC
Confidence 9999999999999999999999863 2899999999999999999999999999
Q ss_pred CcEEEEEEEecCCCCCCEEEEEEEEEcCCccEEEEEEEeecCCC--CceeeEEEEEeCCCCceeeEEEEcceeceeEeC-
Q 017238 217 GQFKLMSYRVKKLKSTPIYVKPQLTSDAGTCRISVMVGIRNDPG--KTIDSIILQFQLPPCILSADLTSNHGTVNVLSN- 293 (375)
Q Consensus 217 G~F~Lm~Y~~~~~~~~P~~v~~~~~~~~~~~~~ei~~~~~~~~~--~~~~~v~I~ip~p~~~~~~~~~~~~G~~~~~~~- 293 (375)
|+|+||+||++...++||.|.|.++.- +..++++.+++++.++ ..+.+|.++||+|+++..++++++.|++ +|.+
T Consensus 283 Ge~ELMkYr~~enInlPFrV~PiV~el-~r~kie~ri~iks~f~~kl~a~~v~~rIPvP~ntv~~n~~v~~Gka-ky~ps 360 (446)
T KOG0938|consen 283 GEFELMKYRVTENINLPFRVTPIVTEL-GRTKIEYRITIKSLFPPKLLAKDVVVRIPVPPNTVKCNISVSNGKA-KYVPS 360 (446)
T ss_pred CceEeEeeeeccCcccceEeeeheecc-cceeEEEEEEEeccCCchhhhcceEEEecCCCccccceeEEecCcc-ccCcc
Confidence 999999999999999999999999854 5799999999999875 3899999999999999999999999999 9999
Q ss_pred -cEEEEEeCCCCCCCCceEEEEEEeecCC--cCCCCCccEEEEEEECceeccccEEeEEEe-e-cCCCcccccEEEEEec
Q 017238 294 -KICTWSIGRIPKDKAPSLSGTMVLETGL--ETLRVFPTFQVEFRIMGVALSGLQIDKLDL-Q-NVPNRLYKGFRAVTRA 368 (375)
Q Consensus 294 -~~l~W~I~~~~~~~~~~l~g~~~~~~~~--~~~~~~~~i~v~F~i~~~s~SGl~V~~l~v-~-~~~~~~~k~vky~t~s 368 (375)
++++|+|.++.|.+|.+++|++++.+.. ...|..|||+++|++|+++.|||.|++++| + +++|+..|||||+|+|
T Consensus 361 en~ivWki~kf~G~tE~tlsAevels~Tt~nkq~WtrPPIsleFeV~MFt~SGL~VrylkV~e~~Sk~~~vkWVrYitka 440 (446)
T KOG0938|consen 361 ENAIVWKINKFNGLTESTLSAEVELSDTTQNKQQWTRPPISLEFEVPMFTNSGLVVRYLKVSEKDSKHRAVKWVRYITKA 440 (446)
T ss_pred cceEEEEecccCCcccceeEEEEEeccCccccccccCCCceeEEeeeeecCCceEEEEEEEecccCCCceEEEEEEeccc
Confidence 9999999999999999999999997654 234789999999999999999999999999 3 5789999999999999
Q ss_pred ccEEEc
Q 017238 369 GEYEVR 374 (375)
Q Consensus 369 g~y~ir 374 (375)
|+||+|
T Consensus 441 GsyEiR 446 (446)
T KOG0938|consen 441 GSYEIR 446 (446)
T ss_pred ceeeeC
Confidence 999998
No 2
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=5.9e-80 Score=568.73 Aligned_cols=370 Identities=52% Similarity=0.865 Sum_probs=352.2
Q ss_pred CCCCceEEeCCEEEEEEEeCCEEEEEEEcCCCChhhHHHHHHHHHHHHhhhcCCCCHHHHHhhHHHHHHHHHhHhhCCcc
Q 017238 4 LKSMPVIASPTHYIFQIVRAGITFLACTQVEMPPLMGIEFLCRVADILSDYLGELNEDLIKDNFVIVYELLDEMIDNGFP 83 (375)
Q Consensus 4 ~~~~Pv~~~~~~~~~~~~~~~l~~v~v~~~~~n~~~~~~~L~~~~~vl~~y~~~l~e~~i~~n~~~i~~llde~id~G~p 83 (375)
++.||++....++++.+.++++||++++..+++|+++++||+++++++++|||+++|.+|++|+..||+|||||+|+|||
T Consensus 44 e~~ppvi~~p~hylfsv~~~~i~~~~~st~e~pPL~~iefL~rv~dv~~eyFg~~s~~~Ik~N~~vv~ell~emiDnGfp 123 (418)
T KOG2740|consen 44 EHVPPVISTPHHYLFSVYRDLIFFCAVSTVETPPLMVIEFLHRVVDVLLEYFGGLSESKIKDNVVVVYELLDEMIDNGFP 123 (418)
T ss_pred ccCCceecCCceeeeeeeccCcEEEEEEeccCCChhHHHHHHHHHHHHHHHhcccCHhHhhcceeeHHHHHHHHHHcCCC
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccChHHHhhhcCCCcchhcccccccCCCCCccCCCCCCCCcCCcccCCCCCcccceEEEEEEEeEEEEEccCCcEEEEE
Q 017238 84 LTTEPNILREMIAPPNIVSKMLSVVTGNSSNVSDILPGATASCVPWRPTDVKYANNEVYVDLVEEMDAIINRDGVLVKCE 163 (375)
Q Consensus 84 ~~t~~~~lk~~i~~~s~~~k~~~~~~g~~~~~~~~~~~~~~~~~~WR~~~~~~~~nei~vdV~E~v~~~~~~~G~i~~~~ 163 (375)
..||+|.||++|+.++++++.++.++| ++|++.++|..+.+.+|||+.+.+|.+||+||||.|+++++++++|.++.++
T Consensus 124 l~tE~NiLke~i~pps~l~~~~~svTg-~~n~~~~lPtg~~s~VPWR~~~~Ky~nNE~yvdvlEeidai~~k~gslv~~e 202 (418)
T KOG2740|consen 124 LVTEPNILKELIPPPSFLSKKFNSVTG-NSNVSDTLPTGALSNVPWRTAGVKYTNNEAYVDVLEEIDAIVDKKGSLVFGE 202 (418)
T ss_pred cccChhHHHhhcCChHHHHHHHhhhhc-cccccccCCCcccccccccccCcccccchhhhhhhheeheEecCCCCEEEEE
Confidence 999999999999999999988999999 7889999999999999999999999999999999999999999999999999
Q ss_pred EEEEEEEEEeeCCCCeeEEEecCCcccccceecceeecCCCCCCceEEEeCCCCcEEEEEEEecC--CCCCCEEEEEEEE
Q 017238 164 IYGEVQVNCLLSGLPDLTLSFANPSILHDVRFHPCVRFRPWESHQILSFVPPDGQFKLMSYRVKK--LKSTPIYVKPQLT 241 (375)
Q Consensus 164 v~G~i~~~~~LsG~P~~~l~ln~~~~l~d~~fH~cV~~~~f~~~~~i~f~PPdG~F~Lm~Y~~~~--~~~~P~~v~~~~~ 241 (375)
|.|.|.|+|.|+|||++.|.|+++..++|++|||||+.++|++++.|+|+||||+|+||+||++. ....|..+..+.+
T Consensus 203 I~g~vd~~~qLsgmPdltlsl~np~~L~dvsfHpcVr~krwe~~~~lsFIPPDGkFrLlsy~v~~~~~v~~pvyv~~~i~ 282 (418)
T KOG2740|consen 203 IQGIVDVCSQLSGMPDLTLSLNNPRLLGDVSFHPCVRYKRWESHSVLSFIPPDGKFRLLSYRVDAQNQVAIPVYVKNSIS 282 (418)
T ss_pred EEEEEEEEEeecCCCceEEEccCccccCCcccccceeecccccccceEEcCCCCcEEEEEEEEehhhccccceEEeeeec
Confidence 99999999999999999999999999999999999999999999999999999999999999986 4567999999999
Q ss_pred EcCCc-cEEEEEEEeecCCCCceeeEEEEEeCCCCceeeEEEEcceeceeEeC--cEEEEEeCCCCCCCCceEEEEEEee
Q 017238 242 SDAGT-CRISVMVGIRNDPGKTIDSIILQFQLPPCILSADLTSNHGTVNVLSN--KICTWSIGRIPKDKAPSLSGTMVLE 318 (375)
Q Consensus 242 ~~~~~-~~~ei~~~~~~~~~~~~~~v~I~ip~p~~~~~~~~~~~~G~~~~~~~--~~l~W~I~~~~~~~~~~l~g~~~~~ 318 (375)
..++. +|++++++.+....+.++-+.|+...|+.+...+...++|+. .++. +.+-|.++++..+.-++|+|+++++
T Consensus 283 l~~~~~~ri~~tvg~~~~~gK~ie~itVt~~~pn~i~~~~k~~~~g~~-~~~~~~k~l~W~~~~i~tg~lp~Lkg~~~~e 361 (418)
T KOG2740|consen 283 LDSNHQGRISLTVGPKKKMGKTIELITVTVQDPNEIAYASKILTHGTF-TNSIIMKQLTWTFGSIATGKLPVLKGTINLE 361 (418)
T ss_pred cCCCceEEEEEeccccccccceeEeEEEEecCccceeeeeccccccee-EeecccceeEEEeecccCCcccccccccccC
Confidence 87655 677777766666668999999999999999999999999999 8888 9999999999988999999999999
Q ss_pred cCCcCCCCCccEEEEEEECceeccccEEeEEEeecCCCcccccEEEEEecccEEEcC
Q 017238 319 TGLETLRVFPTFQVEFRIMGVALSGLQIDKLDLQNVPNRLYKGFRAVTRAGEYEVRS 375 (375)
Q Consensus 319 ~~~~~~~~~~~i~v~F~i~~~s~SGl~V~~l~v~~~~~~~~k~vky~t~sg~y~ir~ 375 (375)
++.....+++.++++|++.+.++||++|+++++.+..|++||||||.|+||++++|+
T Consensus 362 ~~~sk~~~l~t~~Lqykiqg~alsglkVe~Ldm~~~~~k~yKGvKy~t~agnfqvR~ 418 (418)
T KOG2740|consen 362 PGFSKKVDLPTLSLQYKIQGQALSGLKVERLDMYGEPYKPYKGVKYKTKAGNFQVRL 418 (418)
T ss_pred CCCCccccCcccceeeeeeeeeccceEEEeeeecCCCCccccceEEEEeeeeEEEeC
Confidence 888888899999999999999999999999999999999999999999999999995
No 3
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.4e-75 Score=557.96 Aligned_cols=360 Identities=30% Similarity=0.553 Sum_probs=327.4
Q ss_pred CCCCceEEeCCEEEEEEEeCCEEEEEEEcCCCChhhHHHHHHHHHHHHhhhcCCCCHHHHHhhHHHHHHHHHhHhhCCcc
Q 017238 4 LKSMPVIASPTHYIFQIVRAGITFLACTQVEMPPLMGIEFLCRVADILSDYLGELNEDLIKDNFVIVYELLDEMIDNGFP 83 (375)
Q Consensus 4 ~~~~Pv~~~~~~~~~~~~~~~l~~v~v~~~~~n~~~~~~~L~~~~~vl~~y~~~l~e~~i~~n~~~i~~llde~id~G~p 83 (375)
...+|++++++..++|++.+++|++++++.|.+++..++||+++++++.+||+.+.|+.+++|+.++||+|||++|||||
T Consensus 42 ~~~~p~l~~~g~~~~~ik~s~lylv~~~~~n~~a~~v~~~l~~~~~v~~~y~~~l~e~si~~n~vlvyElLde~mDFGyp 121 (424)
T KOG0937|consen 42 DESPPFLVHDGSRFIHIKHSNLYLVAGTRPNVSAALVLSFLYAVADVFGDYLSELEEESIRDNFVLVYELLDEVMDFGYP 121 (424)
T ss_pred CCCCCeEEeCCceEEEEeecceEEEEEeccCCCHHHHHHHHHHHHHHHHHHhccCCccceecchHHHHHHHHHHhccCCc
Confidence 45789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccChHHHhhhcCCCcchhcccccccCCCCCccCCCCCCCCcCCcccCCCCCcccceEEEEEEEeEEEEEccCCcEEEEE
Q 017238 84 LTTEPNILREMIAPPNIVSKMLSVVTGNSSNVSDILPGATASCVPWRPTDVKYANNEVYVDLVEEMDAIINRDGVLVKCE 163 (375)
Q Consensus 84 ~~t~~~~lk~~i~~~s~~~k~~~~~~g~~~~~~~~~~~~~~~~~~WR~~~~~~~~nei~vdV~E~v~~~~~~~G~i~~~~ 163 (375)
|.|+...|++||.++++ ++.. .+.+.|.+.+.+++||+.+++|+|||+|+||+|++++.++++|.++.++
T Consensus 122 Q~t~s~iL~~yi~~~~~--~l~~--------~~~~~p~avtnavsWrs~gi~~~KnevflDViE~Vs~l~~~~G~vl~s~ 191 (424)
T KOG0937|consen 122 QTTDSEILKNYITQKAN--RLQD--------AQPRPPLAVTNAVSWRSEGIYYGKNEVFLDVIESVSLLYDSNGIVLLSE 191 (424)
T ss_pred ccchHHHHHHHhccccc--ceee--------cCCCCCcccccceeecccccccccceEEEEhhhhhhHhhhcCCcEEEee
Confidence 99999999999999854 2221 1113466778888999999999999999999999999999999999999
Q ss_pred EEEEEEEEEeeCCCCeeEEEecCCc--------------ccccceecceeecCCCCCCceEEEeCCCCcEEEEEEEecCC
Q 017238 164 IYGEVQVNCLLSGLPDLTLSFANPS--------------ILHDVRFHPCVRFRPWESHQILSFVPPDGQFKLMSYRVKKL 229 (375)
Q Consensus 164 v~G~i~~~~~LsG~P~~~l~ln~~~--------------~l~d~~fH~cV~~~~f~~~~~i~f~PPdG~F~Lm~Y~~~~~ 229 (375)
|.|+|+|||+|+|||+++|++|+.. .++|++||+||++++|+.+|.|+|+||||+|+||+||++..
T Consensus 192 i~G~I~~k~~LsGmPelrl~ln~~~~~~~~~~~~~s~~v~ledi~fh~~v~l~~fd~dr~i~FiPPdGeF~Lm~Y~ls~~ 271 (424)
T KOG0937|consen 192 IVGTIKLKCYLSGMPELRLGLNDKVLFDKQGPRSKSKGVELEDIKFHECVRLSRFDNDRTISFIPPDGEFELMRYRLSTH 271 (424)
T ss_pred eeeEEEEEEEcCCCceeeeecCcccccccccccccCcceEeeecccceeechhhccCCceEEecCCCCceEEEEEEecCC
Confidence 9999999999999999999999742 37899999999999999999999999999999999999987
Q ss_pred CCCCEEEEEEEEEcCCccEEEEEEEeecCCCC--ceeeEEEEEeCCCCceeeEEEEcceeceeEeC--cEEEEEeCCCCC
Q 017238 230 KSTPIYVKPQLTSDAGTCRISVMVGIRNDPGK--TIDSIILQFQLPPCILSADLTSNHGTVNVLSN--KICTWSIGRIPK 305 (375)
Q Consensus 230 ~~~P~~v~~~~~~~~~~~~~ei~~~~~~~~~~--~~~~v~I~ip~p~~~~~~~~~~~~G~~~~~~~--~~l~W~I~~~~~ 305 (375)
.. |+.-.+++....+..++++.++++++++. .+++|+|+||+|...+++.++++.|++ +|.. ++++|+|+++++
T Consensus 272 vk-Pli~~~~~~~~~~~~ri~i~~K~~~~fk~~~~a~~v~I~iP~P~~a~~~~fk~s~G~~-~~~~e~~~l~W~I~~~~g 349 (424)
T KOG0937|consen 272 VK-PLIWFYQLIEEHSRSRIEVMVKLREQFKSRSSANNVEICIPVPDDASSPSFKTSLGSA-KYDPEKSALRWTIKKFVG 349 (424)
T ss_pred CC-CeEEeeeeeeeccceeEEEEEechhhcCCccccceEEEEeeCCCccccceEeccCCce-eeecccceEEEEeccccC
Confidence 77 66655666666678999999999998864 999999999999999999999999999 9988 999999999999
Q ss_pred CCCceEEEEEEeecCCcCC---CCCccEEEEEEECceeccccEEeEEEee--cCCCcccccEEEEEecccEEEcC
Q 017238 306 DKAPSLSGTMVLETGLETL---RVFPTFQVEFRIMGVALSGLQIDKLDLQ--NVPNRLYKGFRAVTRAGEYEVRS 375 (375)
Q Consensus 306 ~~~~~l~g~~~~~~~~~~~---~~~~~i~v~F~i~~~s~SGl~V~~l~v~--~~~~~~~k~vky~t~sg~y~ir~ 375 (375)
+.+..+++++.+.+...++ ...+|++|+|+||+++.||++|+++++. ..+|++.+||||.|+||.|++|.
T Consensus 350 g~e~~~r~~~~lp~~~~e~~~~~~~~pi~v~FeIp~~T~SgiqVrylki~ep~~~y~s~~WVRy~T~s~~Y~~r~ 424 (424)
T KOG0937|consen 350 GKEYSLRARMDLPSEEHEEQCTEGLGPIKVKFEIPYFTVSGIQVRYLKIIEPKSQYQSLPWVRYNTQSGPYEIRV 424 (424)
T ss_pred CceEEEEEeecCCccccCCCCcccCCceEEEEEecccccCCeEEEEEEecccccCCCccceEEEEccCCceEeeC
Confidence 9999999999996543332 4588999999999999999999999993 46899999999999999999985
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=9.8e-60 Score=442.10 Aligned_cols=247 Identities=35% Similarity=0.715 Sum_probs=211.4
Q ss_pred CcccCCCCCcccceEEEEEEEeEEEEEccCCcEEEEEEEEEEEEEEeeCCCCeeEEEecCC-------cccccceeccee
Q 017238 127 VPWRPTDVKYANNEVYVDLVEEMDAIINRDGVLVKCEIYGEVQVNCLLSGLPDLTLSFANP-------SILHDVRFHPCV 199 (375)
Q Consensus 127 ~~WR~~~~~~~~nei~vdV~E~v~~~~~~~G~i~~~~v~G~i~~~~~LsG~P~~~l~ln~~-------~~l~d~~fH~cV 199 (375)
+|||+.+++|++|||||||+|+++|+++++|.+..++|.|+|.|+|+|+|+|+|+|+|+++ ..++|++|||||
T Consensus 1 ~~wR~~~~~~~~nei~vdv~E~i~~~~~~~G~~~~~~v~G~v~~~~~l~g~p~i~l~l~~~~~~~~~~~~l~~~~fH~cV 80 (262)
T PF00928_consen 1 VPWRPSGIKYKKNEIFVDVVEKISAVLDRDGNILSSEVKGSVQCKSFLSGMPEIKLTLNNPLVVSKNGIKLDDVSFHPCV 80 (262)
T ss_dssp -TTS-STB--SSEEEEEEEEEEEEEEEETTSEEEEEEEEEEEEEEEE-SST-EEEEEESSSCCCTSSSBEESEEEEETTE
T ss_pred CCcccCCcccccceEEEEEEEEEEEEEccCCcEEEEEEEEEEEEEEeCCCCCeEEEEecCccccccCceeeeceeecccc
Confidence 6899999999999999999999999999999999999999999999999999999999998 679999999999
Q ss_pred ecCCCCCCceEEEeCCCCcEEEEEEEecCCCCCCEEEEEEEEEcCCccEEEEEEEeecCCCC--ceeeEEEEEeCCCCce
Q 017238 200 RFRPWESHQILSFVPPDGQFKLMSYRVKKLKSTPIYVKPQLTSDAGTCRISVMVGIRNDPGK--TIDSIILQFQLPPCIL 277 (375)
Q Consensus 200 ~~~~f~~~~~i~f~PPdG~F~Lm~Y~~~~~~~~P~~v~~~~~~~~~~~~~ei~~~~~~~~~~--~~~~v~I~ip~p~~~~ 277 (375)
+++.|++++.|+|+||||+|+||+||++....+||.++|++.. .+++++++.++++.+... .+++|.|+||+|..+.
T Consensus 81 ~~~~~~~~~~i~f~PPdg~f~Ll~Yr~~~~~~~P~~i~~~~~~-~~~~~~~v~i~~~~~~~~~~~~~~v~I~iplP~~~~ 159 (262)
T PF00928_consen 81 DLSKFESDRVISFIPPDGEFTLLRYRVSSNSPLPFKITCWVSE-KSSGRFEVTIELESNFPNKISLENVVIRIPLPPGTS 159 (262)
T ss_dssp ECCCCCSHTEEEE---SEEEEEEEEEEESSS--SEEEEEEEEE-ETTTEEEEEEEEEE-S-TTSEEEEEEEEEE--TTEE
T ss_pred CccccccccceecCCCCceEEEEEEEccCCCCCCcEEEEEecc-CCCceEEEEEEecccCCCCceeceEEEEeecCCccc
Confidence 9999999999999999999999999999888999999999997 457899999999876654 8999999999999999
Q ss_pred eeEEEEcceeceeEeC--cEEEEEeCCCCCCCCceEEEEEEeecCCcCCC--CCccEEEEEEECceeccccEEeEEEeec
Q 017238 278 SADLTSNHGTVNVLSN--KICTWSIGRIPKDKAPSLSGTMVLETGLETLR--VFPTFQVEFRIMGVALSGLQIDKLDLQN 353 (375)
Q Consensus 278 ~~~~~~~~G~~~~~~~--~~l~W~I~~~~~~~~~~l~g~~~~~~~~~~~~--~~~~i~v~F~i~~~s~SGl~V~~l~v~~ 353 (375)
.++++++.|++ +|+. ++++|+|++++++.+++++|+++|......+. .++||+|+|++|++++||++|++++|.+
T Consensus 160 ~~~~~~~~G~~-~~~~~~~~l~W~I~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~pi~v~F~~~~~~~Sgl~V~~l~v~~ 238 (262)
T PF00928_consen 160 SPSIESSDGSA-EYDEEENALVWKIKKLPGGSESTLSGTLEFSSPSSVPSDWSFFPISVEFTIPGYTLSGLKVRSLDVVN 238 (262)
T ss_dssp EEEEEESSSEE-EEETGCTEEEEEEEEEETSEEEEEEEEEEEEEECCSS-S-----EEEEEEESTSETTT-EEEEEEEE-
T ss_pred cceeeecCceE-EEEccCCEEEEEECCccCcccccEEEEEEecCCCcccccccceeEEEEEEeCCcccCCCEEEEEEeEe
Confidence 99999999999 9999 99999999999999999999999976554433 6889999999999999999999999965
Q ss_pred --CCCcccccEEEEEecccEEEcC
Q 017238 354 --VPNRLYKGFRAVTRAGEYEVRS 375 (375)
Q Consensus 354 --~~~~~~k~vky~t~sg~y~ir~ 375 (375)
.+++++|||||.|+||+|+||+
T Consensus 239 ~~~~~~~~k~vky~t~s~~Y~iR~ 262 (262)
T PF00928_consen 239 EDENYKPYKWVKYVTKSGSYEIRT 262 (262)
T ss_dssp SSCGGGSEEEEEEEEEEEEEEE--
T ss_pred cCCCCCCcccEEEEEEcCcEEEcC
Confidence 7899999999999999999996
No 5
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.6e-41 Score=320.68 Aligned_cols=356 Identities=18% Similarity=0.281 Sum_probs=287.6
Q ss_pred ceEEeCCEEEEEEEeCCEEEEEEEcCCCChhhHHHHHHHHHHHHhhhcCCCCHHHHHhhHHHHHHHHHhHhhCCcccccC
Q 017238 8 PVIASPTHYIFQIVRAGITFLACTQVEMPPLMGIEFLCRVADILSDYLGELNEDLIKDNFVIVYELLDEMIDNGFPLTTE 87 (375)
Q Consensus 8 Pv~~~~~~~~~~~~~~~l~~v~v~~~~~n~~~~~~~L~~~~~vl~~y~~~l~e~~i~~n~~~i~~llde~id~G~p~~t~ 87 (375)
-+++.+...++|...+++|+|++|+.++|++.++++|+.|.+++.+||..+.|..|.+|.+.+...|||++..||.++.+
T Consensus 47 T~vEt~~VRYVYqP~d~lY~vLITtk~SNIleDl~TL~Lfskvipey~~slde~eI~~~~FelifAFDEivsLGyre~v~ 126 (512)
T KOG2635|consen 47 TFVETDSVRYVYQPLDNLYIVLITTKQSNILEDLETLRLFSKVIPEYCSSLDEKEILENAFELIFAFDEIVSLGYRENVN 126 (512)
T ss_pred cEEecccEEEEEEecccEEEEEEeccccchhhHHHHHHHHHHhchhhhhhhhHHHHHHhhhhhhhccchhhhhccccccc
Confidence 46677888999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHhhhcCCCcchhccccccc----------------------------C-C-------------CC----C-cc----
Q 017238 88 PNILREMIAPPNIVSKMLSVVT----------------------------G-N-------------SS----N-VS---- 116 (375)
Q Consensus 88 ~~~lk~~i~~~s~~~k~~~~~~----------------------------g-~-------------~~----~-~~---- 116 (375)
.-++|+|..|+||++|++..+. | + ++ + .+
T Consensus 127 laQikty~eMdSHEEKi~e~v~~nke~ea~q~mkrKaKElqr~r~ea~rrgg~~~~~~~~~~s~g~~~~s~~~~~~~~~~ 206 (512)
T KOG2635|consen 127 LAQIKTYLEMDSHEEKIHELVMRNKEREAKQEMKRKAKELQRARKEAERRGGSLNPGFDAIGSSGYSSVSTTNAINRVES 206 (512)
T ss_pred HHHhhhhhccccHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhhhccccccCCCccccccccccCCcccchhhcccc
Confidence 9999999999999999876430 1 0 00 0 00
Q ss_pred -CCCC---C-CCCcCCc-----------------------------------cc------CCCCCcccceEEEEEEEeEE
Q 017238 117 -DILP---G-ATASCVP-----------------------------------WR------PTDVKYANNEVYVDLVEEMD 150 (375)
Q Consensus 117 -~~~~---~-~~~~~~~-----------------------------------WR------~~~~~~~~nei~vdV~E~v~ 150 (375)
...| + ...+..| -+ +......++.+++.+.|+++
T Consensus 207 ~~~~~~~~sa~~~~s~pak~mklG~k~~~s~~~~d~Lk~ege~ia~~~s~~g~~s~aap~~~~p~v~~e~v~i~ieEkln 286 (512)
T KOG2635|consen 207 IAQKPKQQSAAKASSAPAKAMKLGKKTKNSDTFVDKLKGEGERIAGASSAIGSASSAAPPPTAPDVPEESVHIVIEEKLN 286 (512)
T ss_pred ccccccccccccCCCCCchhhhhcccccchhhHHHHhhccccccccccccccccccCCCCCCCCCCccceEEEEEeeeEe
Confidence 0000 0 0000000 00 00111234559999999999
Q ss_pred EEEccCCcEEEEEEEEEEEEEEeeCCCCeeEEEecCC-cccccceecceeecCCCCCCceEEEeCCCCcEE------EEE
Q 017238 151 AIINRDGVLVKCEIYGEVQVNCLLSGLPDLTLSFANP-SILHDVRFHPCVRFRPWESHQILSFVPPDGQFK------LMS 223 (375)
Q Consensus 151 ~~~~~~G~i~~~~v~G~i~~~~~LsG~P~~~l~ln~~-~~l~d~~fH~cV~~~~f~~~~~i~f~PPdG~F~------Lm~ 223 (375)
+.+++||.+.++++.|.+.++....-...+.|.|++. ..--++++||++|++.|.++..|.+.+|+..|+ |++
T Consensus 287 ~~~~RDGgi~s~E~qG~lsLrI~d~e~~~i~lkl~n~~~~g~q~ktHPNlDK~~f~s~s~iglk~~~K~FPvn~~VGvLk 366 (512)
T KOG2635|consen 287 VRLSRDGGIKSGEVQGTLSLRIKDEEYGDIELKLANGRDKGTQLKTHPNLDKKVFLSSSLIGLKRPEKPFPVNSDVGVLK 366 (512)
T ss_pred EEEcccCCccceeeeeeEEEEEccccccceEEEEcCCCCcceeeeeCCCcchhhhccccccccccCCCCCCcCCcceEEE
Confidence 9999999999999999999999999889999999763 346678999999999999999999999999996 799
Q ss_pred EEecC--CCCCCEEEEEEEEEcCCccEEEEEEEeecCCCCceeeEEEEEeCCCCceeeEEEEcceeceeEeC--cEEEEE
Q 017238 224 YRVKK--LKSTPIYVKPQLTSDAGTCRISVMVGIRNDPGKTIDSIILQFQLPPCILSADLTSNHGTVNVLSN--KICTWS 299 (375)
Q Consensus 224 Y~~~~--~~~~P~~v~~~~~~~~~~~~~ei~~~~~~~~~~~~~~v~I~ip~p~~~~~~~~~~~~G~~~~~~~--~~l~W~ 299 (375)
||... ....|++++||++...++ +++.+.++....-.++||.|.||+|.++ .+++...+|.+ .|+. +.++|+
T Consensus 367 WR~~~~des~iPlTincWPSes~~g--~dV~iEYe~~~~~eL~dV~i~iPlP~~i-apsv~~~Dge~-~~~~~~~~leW~ 442 (512)
T KOG2635|consen 367 WRMVDEDESEIPLTINCWPSESGNG--YDVNIEYEAVLECELNDVIITIPLPANI-APSVGECDGEY-RYDERKNVLEWS 442 (512)
T ss_pred EeecccccccCceEEEeccccCCCC--eEEEEEEeehhcccccceEEEeeccccc-CCccceecceE-EeccccceeEEE
Confidence 99976 577899999999876533 5555555543234899999999999998 88999999999 9998 999999
Q ss_pred eCCCCCCCCceEEEEEEeecCCcCCCCCccEEEEEEECceeccccEEeEEEeecCCCccccc-EEEEEecccEEE
Q 017238 300 IGRIPKDKAPSLSGTMVLETGLETLRVFPTFQVEFRIMGVALSGLQIDKLDLQNVPNRLYKG-FRAVTRAGEYEV 373 (375)
Q Consensus 300 I~~~~~~~~~~l~g~~~~~~~~~~~~~~~~i~v~F~i~~~s~SGl~V~~l~v~~~~~~~~k~-vky~t~sg~y~i 373 (375)
|+.+. .+.+|+++|+.....++.++|++|.|+.. .+++|+.|.++.-.++. .+.+. ++=+-.+..|+|
T Consensus 443 I~~Ia----~N~SGslEFs~~~~~~~~fFPl~VsF~s~-~~ftgl~vqkVv~~~~~-~~~~y~~~t~f~~dky~V 511 (512)
T KOG2635|consen 443 IGVIA----KNFSGSLEFSCPASDPDGFFPLSVSFTSD-TVFTGLFVQKVVRNDGH-APVRYSVETTFEVDKYEV 511 (512)
T ss_pred eeeec----cCCCCcEEEeecCCCCCceeeEEEEEEec-ccccceEEEEEEEcCCC-CCceeEEEEEEEeeeeEe
Confidence 99983 35789999988788889999999999999 59999999998763332 22222 333344677775
No 6
>KOG2677 consensus Stoned B synaptic vesicle biogenesis protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.2e-34 Score=283.57 Aligned_cols=236 Identities=22% Similarity=0.410 Sum_probs=203.8
Q ss_pred CCCcccceEEEEEEEeEEEEEccCCcEEEEEEEEEEEEEEeeCCCCeeEEEecCCc---------------------ccc
Q 017238 133 DVKYANNEVYVDLVEEMDAIINRDGVLVKCEIYGEVQVNCLLSGLPDLTLSFANPS---------------------ILH 191 (375)
Q Consensus 133 ~~~~~~nei~vdV~E~v~~~~~~~G~i~~~~v~G~i~~~~~LsG~P~~~l~ln~~~---------------------~l~ 191 (375)
...|..+||.|||.+..++.++++|.++...|..+|.|.|+|+|.++|.|+|||.. .+.
T Consensus 581 k~nY~e~EI~v~~~Defsg~V~Keg~~~~~~v~tri~cL~FlsG~~ec~lgLND~~~kg~Eiv~rkDimp~~t~kwI~~~ 660 (922)
T KOG2677|consen 581 KSNYLEEEITVDVRDEFSGIVSKEGQILQHHVLTRIHCLSFLSGLAECRLGLNDILVKGNEIVLRKDIMPTTTTKWIKLH 660 (922)
T ss_pred ccccccceeEEEEEeccceeecccchhhhhhhhhhhhhhhhccCCceeEeecchhhhcccceeEeccccccccccceeee
Confidence 34688999999999999999999999999999999999999999999999999753 388
Q ss_pred cceecceeecCCCCCCceEEEeCCCC-cEEEEEEEecC-CCCCCEEEEEEEEEcCCccEEEEEEEeec------CC----
Q 017238 192 DVRFHPCVRFRPWESHQILSFVPPDG-QFKLMSYRVKK-LKSTPIYVKPQLTSDAGTCRISVMVGIRN------DP---- 259 (375)
Q Consensus 192 d~~fH~cV~~~~f~~~~~i~f~PPdG-~F~Lm~Y~~~~-~~~~P~~v~~~~~~~~~~~~~ei~~~~~~------~~---- 259 (375)
+|.||.||+.+.|+++|+|.|.|||| .|+|||||+.. ...+||+++-.++.+ |.++|++..++. +.
T Consensus 661 ~~~FH~cVn~~eF~~srVI~F~PlDaCrFElMRFrt~~~~~~lpftlks~~~V~--Ga~VEvq~~~~mat~~qr~rd~~~ 738 (922)
T KOG2677|consen 661 ECRFHGCVNEDEFHNSRVILFNPLDACRFELMRFRTVFAEKTLPFTLKSATSVN--GAEVEVQSWLRMATGFQRNRDPLT 738 (922)
T ss_pred eeeeecccchhhccccceEEecCcccceeeeeeeeeecCCCcCceeeeeeeeec--cceeehHHHHHHHhhhhhccCccc
Confidence 99999999999999999999999999 79999999975 457899999888865 567777553331 11
Q ss_pred CCceeeEEEEEeCCCCcee--------------------------------eEEEEcceeceeEeC--cEEEEEeCCCCC
Q 017238 260 GKTIDSIILQFQLPPCILS--------------------------------ADLTSNHGTVNVLSN--KICTWSIGRIPK 305 (375)
Q Consensus 260 ~~~~~~v~I~ip~p~~~~~--------------------------------~~~~~~~G~~~~~~~--~~l~W~I~~~~~ 305 (375)
..+|+|+.|++|+|..|.. +.++++.|++ +|++ +.++|+|++++.
T Consensus 739 ~vpCenI~IrfPVPs~WIk~fr~e~~~g~kSlkaK~nR~a~~gsl~~~~sepvi~vt~G~A-KYEhay~siVWrI~RLPd 817 (922)
T KOG2677|consen 739 QVPCENIMIRFPVPSEWIKNFRRESVLGEKSLKAKVNRGASFGSLSVSGSEPVIRVTLGTA-KYEHAYNSIVWRINRLPD 817 (922)
T ss_pred cCcccceeEeccCcHHHHHHHHHHhhhccchhhhhhcccccccchhhccCCceEEEeecch-hhHHhhhhheeecccCCc
Confidence 1399999999999987741 3588899999 9999 999999999975
Q ss_pred -----CCCceEEEEEEeecCCcCCCC-CccEEEEEEECceeccccEEeEEEeecCCCcccccEEEEEecccEEE
Q 017238 306 -----DKAPSLSGTMVLETGLETLRV-FPTFQVEFRIMGVALSGLQIDKLDLQNVPNRLYKGFRAVTRAGEYEV 373 (375)
Q Consensus 306 -----~~~~~l~g~~~~~~~~~~~~~-~~~i~v~F~i~~~s~SGl~V~~l~v~~~~~~~~k~vky~t~sg~y~i 373 (375)
+..++|.|.+++++..+.+.+ .+++.|+|++|..++|...|+++.|+. ...+.|||+|.++ .+|++
T Consensus 818 Knsa~~hpHcl~c~lELgSd~evPs~f~p~~~V~FsmP~t~aS~t~VRSisVE~-~~~v~K~V~y~A~-Y~yqv 889 (922)
T KOG2677|consen 818 KNSASGHPHCLFCHLELGSDREVPSRFAPHVNVEFSMPTTSASKTSVRSISVED-KTDVRKWVNYSAH-YSYQV 889 (922)
T ss_pred cccccCCCeeEEEEEeccccccCchhhccccceeeeccccccccceeeeeeccc-cccHHHHHhhhhh-eeeee
Confidence 357899999999887777766 468999999999999999999999965 5679999999876 56654
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=99.74 E-value=1.4e-17 Score=141.75 Aligned_cols=94 Identities=31% Similarity=0.542 Sum_probs=86.9
Q ss_pred CCCceEEeCCEEEEEEEeCCEEEEEEEcCCCChhhHHHHHHHHHHHHhhhcCCCCHHHHHhhHHHHHHHHHhHhhCCccc
Q 017238 5 KSMPVIASPTHYIFQIVRAGITFLACTQVEMPPLMGIEFLCRVADILSDYLGELNEDLIKDNFVIVYELLDEMIDNGFPL 84 (375)
Q Consensus 5 ~~~Pv~~~~~~~~~~~~~~~l~~v~v~~~~~n~~~~~~~L~~~~~vl~~y~~~l~e~~i~~n~~~i~~llde~id~G~p~ 84 (375)
+.+|++.++++.++|++.+++||+++++.+.|+++.+++|+.+.++|++|||+++|..|.+|+..+|++||||+|+|+|+
T Consensus 45 ~~~~i~~~~~~~~vy~~~~dl~~~~v~~~~eNel~~~e~l~~~v~~l~~~~~~v~e~~i~~N~~~v~~~LDEiid~G~i~ 124 (141)
T PF01217_consen 45 KQSPIFEHDNYRIVYKRYSDLYFVVVGDENENELLLLEFLHRLVEVLDDYFGNVSEKDILENFDLVYLILDEIIDGGIIL 124 (141)
T ss_dssp SSTSEEEETTEEEEEEEETTEEEEEEESSTSBHHHHHHHHHHHHHHHHHHHSS-SHHHHHHTHHHHHHHHHHHEETTEES
T ss_pred ccceeeecccceeeeEeeccEEEEEEeecccchHHHHHHHHHhhhhhhhhhccccHHHHHHCHHHHHHHHHHHHhCCEEE
Confidence 56899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccChHHHhhhcCCC
Q 017238 85 TTEPNILREMIAPP 98 (375)
Q Consensus 85 ~t~~~~lk~~i~~~ 98 (375)
+|+++.|...+.+.
T Consensus 125 etd~~~I~~~v~~~ 138 (141)
T PF01217_consen 125 ETDPNVILKRVTMQ 138 (141)
T ss_dssp --THHHHHHHHHHC
T ss_pred ECCHHHHHHHHHHh
Confidence 99999998877643
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=99.27 E-value=2.7e-09 Score=99.53 Aligned_cols=226 Identities=19% Similarity=0.252 Sum_probs=132.5
Q ss_pred EEEEEEEeEEEEEccCCcEEEEEEEEEEEEEEeeC------CCCeeEEEecCCcccccceecceeecCCCCCCceEEEeC
Q 017238 141 VYVDLVEEMDAIINRDGVLVKCEIYGEVQVNCLLS------GLPDLTLSFANPSILHDVRFHPCVRFRPWESHQILSFVP 214 (375)
Q Consensus 141 i~vdV~E~v~~~~~~~G~i~~~~v~G~i~~~~~Ls------G~P~~~l~ln~~~~l~d~~fH~cV~~~~f~~~~~i~f~P 214 (375)
+-.-++|+|||.+. +|.+....|.|+|.+.-.-. ..+.+.+.|++...|+.+...+..=...-.++....|.+
T Consensus 3 l~asi~E~VnA~Fk-~g~~~~v~v~GEv~ls~~~~~~~~~~~~~~l~~rl~n~~~le~i~pN~~~v~~~~~~~~~f~~n~ 81 (257)
T PF10291_consen 3 LNASITETVNAYFK-GGQLSKVKVTGEVALSYPAGISSSLTSPPPLSFRLNNFSRLEKIAPNPQFVSSSSQSDGEFWLNM 81 (257)
T ss_dssp EEEEEEEEEEEEEE-TTEEEEEEEEEEEEEEEE--SSS-----SEEEEEEETGGGEEEEEE-TTTE--EEEETTEEEE-T
T ss_pred eeEEEEEEEEEEEE-CCcEEEEEEEEEEEEecCCChhhcccCCCcEEEEEcCcchhceeecCHhHeecCCCCCCcEEEeh
Confidence 45678999999996 78999999999999875432 245778999888777776555432211111233466655
Q ss_pred CC--CcE--EEEEEEecCC----CCCCEEEEEEEEEcCCccEEEEEEEeec-CCC--CceeeEEEEEeCCCC-ceeeEEE
Q 017238 215 PD--GQF--KLMSYRVKKL----KSTPIYVKPQLTSDAGTCRISVMVGIRN-DPG--KTIDSIILQFQLPPC-ILSADLT 282 (375)
Q Consensus 215 Pd--G~F--~Lm~Y~~~~~----~~~P~~v~~~~~~~~~~~~~ei~~~~~~-~~~--~~~~~v~I~ip~p~~-~~~~~~~ 282 (375)
+. ... ..++|++... ...|+.+.+..+..+....+-+.+++.+ ... ..++||.|.+++... ..+++..
T Consensus 82 ~~l~~~~~~~alKYqv~~~~~~~~~~Pl~l~~~Wk~e~~~tsl~l~Y~~Np~~~~~~~~L~nv~~~v~l~g~~~ts~~sk 161 (257)
T PF10291_consen 82 SALTSHLPKQALKYQVHSDPSNLSSVPLILKPVWKCEPSQTSLILDYKLNPDAFASPVPLENVVFSVPLDGGRATSAQSK 161 (257)
T ss_dssp TTTBT-E-EEEEEEEEES--------SEEEEEEEEE-SSEEEEEEEEEE-TTT--E-EEEEEEEEEEEB-SS-EEEEEES
T ss_pred HHhhhhhhhceEEEEEeccccccCCCCeEEEeEEEeCCceEEEEEEEEeChhhccccceeeeEEEEEEcCCccccccccC
Confidence 53 333 5799999863 5679999998888764444444444444 222 389999999999887 5554443
Q ss_pred EcceeceeEeCcEEEEEeCCCCC--CCC-ceEEEEEEeecCCcCCCCCccEEEEEEEC-ceeccccEEeEEEee------
Q 017238 283 SNHGTVNVLSNKICTWSIGRIPK--DKA-PSLSGTMVLETGLETLRVFPTFQVEFRIM-GVALSGLQIDKLDLQ------ 352 (375)
Q Consensus 283 ~~~G~~~~~~~~~l~W~I~~~~~--~~~-~~l~g~~~~~~~~~~~~~~~~i~v~F~i~-~~s~SGl~V~~l~v~------ 352 (375)
..|++ .=+.+.+.|+++.+.- +.+ ..|.|.|...... ..-.+|.+.|++. +.+.||+.|.-..-.
T Consensus 162 -P~g~~-~~e~~ri~Wrl~el~~~~~~~~~kL~ARf~~~~~~---~~p~~v~vkF~~~~~~~~sg~~i~~~~~~~~~dp~ 236 (257)
T PF10291_consen 162 -PQGTW-NKEKNRITWRLPELSLTSEGEGGKLIARFMTSGGP---SRPGGVEVKFEIEGGSTLSGLGISLVYQDDEEDPP 236 (257)
T ss_dssp -SS--B--SSS-EEEEE-SSEEEETT---EEEEEEEEESS-------SS-EEEEEEE---S-SS----EEEEEESSS-TT
T ss_pred -CCccc-cCCCcEEEEECCcccccCCCCCceEEEEEECCCCC---CCCceEEEEEEEcCCCcccCcEEEEeecccccCCC
Confidence 34777 4334999999999742 222 6899998886533 2567899999999 888999888877211
Q ss_pred cCCCcccccEEEEEecccEEE
Q 017238 353 NVPNRLYKGFRAVTRAGEYEV 373 (375)
Q Consensus 353 ~~~~~~~k~vky~t~sg~y~i 373 (375)
+..|+.. -++-...||+|..
T Consensus 237 ~~~w~~~-~~~r~~~sGkY~~ 256 (257)
T PF10291_consen 237 GGGWRLV-LVKRKLVSGKYIA 256 (257)
T ss_dssp ----EE--EEEEEEEEEEEE-
T ss_pred CCcceEE-EEEEEEeeeEEec
Confidence 2234443 4777778999973
No 9
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=98.97 E-value=1.8e-09 Score=88.25 Aligned_cols=86 Identities=26% Similarity=0.303 Sum_probs=79.4
Q ss_pred ceEEeCCEEEEEEEeCCEEEEEEEcCCCChhhHHHHHHHHHHHHhhhcCCCCHHHHHhhHHHHHHHHHhHhhCCcccccC
Q 017238 8 PVIASPTHYIFQIVRAGITFLACTQVEMPPLMGIEFLCRVADILSDYLGELNEDLIKDNFVIVYELLDEMIDNGFPLTTE 87 (375)
Q Consensus 8 Pv~~~~~~~~~~~~~~~l~~v~v~~~~~n~~~~~~~L~~~~~vl~~y~~~l~e~~i~~n~~~i~~llde~id~G~p~~t~ 87 (375)
-+.+..+..++|++..+|||+.+.+.+.|-+.+++++|.|.+++..|||++.|-.+..||-.+|.+||||+-+|..++++
T Consensus 48 N~~e~k~~kiVYrrYA~LyF~f~Vd~~dnEl~iL~lIh~FVE~lDr~FgnVCELdlIFNF~kv~~ILdE~i~gG~i~Es~ 127 (152)
T COG5030 48 NFIEGKNEKIVYRRYATLYFVFGVDNDDNELIILELIHNFVEILDRFFGNVCELDLIFNFQKVYAILDEMILGGEIIESS 127 (152)
T ss_pred ccccccCcEEEeeecCcEEEEEEEcCCCCcchHHHHHHHHHHHHHHHhccceeeEeEeeHHHHHHHHHHHHhCCeeeecC
Confidence 35566677888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHhh
Q 017238 88 PNILRE 93 (375)
Q Consensus 88 ~~~lk~ 93 (375)
++.+-.
T Consensus 128 ~~~vl~ 133 (152)
T COG5030 128 KNEVLE 133 (152)
T ss_pred HHHHHH
Confidence 877553
No 10
>KOG0934 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.93 E-value=7.9e-10 Score=90.22 Aligned_cols=85 Identities=25% Similarity=0.248 Sum_probs=78.6
Q ss_pred CCCceEEeCCEEEEEEEeCCEEEEEEEcCCCChhhHHHHHHHHHHHHhhhcCCCCHHHHHhhHHHHHHHHHhHhhCCccc
Q 017238 5 KSMPVIASPTHYIFQIVRAGITFLACTQVEMPPLMGIEFLCRVADILSDYLGELNEDLIKDNFVIVYELLDEMIDNGFPL 84 (375)
Q Consensus 5 ~~~Pv~~~~~~~~~~~~~~~l~~v~v~~~~~n~~~~~~~L~~~~~vl~~y~~~l~e~~i~~n~~~i~~llde~id~G~p~ 84 (375)
+.+-.++.+++.++|++.+++||++....+.|-+.+++++|++.++|..|||++.|-.|..||..+|.+|||++-.|-.+
T Consensus 45 k~csfie~kd~kvVyrryasl~f~~~v~~~dNEL~~LE~IH~~vE~lDkYFg~VCELDiiFNfekay~ILde~~~~g~~~ 124 (145)
T KOG0934|consen 45 KMCSFIEYKDEKVVYRRYASLFFCVGVEDNDNELAILEFIHNYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEIQ 124 (145)
T ss_pred ccccchhccCceehhhhhhhEEEEEEEecCCchhhHHHHHHHHHHHHHHHhccceeeEEEEehHhHHHHHHHHhcCcchH
Confidence 45567888999999999999999999999999999999999999999999999999999999999999999999999877
Q ss_pred ccChH
Q 017238 85 TTEPN 89 (375)
Q Consensus 85 ~t~~~ 89 (375)
++..+
T Consensus 125 e~~k~ 129 (145)
T KOG0934|consen 125 ETSKN 129 (145)
T ss_pred hhhcc
Confidence 76644
No 11
>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.74 E-value=2.4e-08 Score=79.57 Aligned_cols=80 Identities=24% Similarity=0.312 Sum_probs=72.6
Q ss_pred CCEEEEEEEeCCEEEEEEEcCCCChhhHHHHHHHHHHHHhhhcCCCCHHHHHhhHHHHHHHHHhHhhCCcccccChHHHh
Q 017238 13 PTHYIFQIVRAGITFLACTQVEMPPLMGIEFLCRVADILSDYLGELNEDLIKDNFVIVYELLDEMIDNGFPLTTEPNILR 92 (375)
Q Consensus 13 ~~~~~~~~~~~~l~~v~v~~~~~n~~~~~~~L~~~~~vl~~y~~~l~e~~i~~n~~~i~~llde~id~G~p~~t~~~~lk 92 (375)
....+++++.++|||+.+.+...|.+..++.+|.+.++|..||+++.|-.+..||..+|.++|||+-+|..++|+...+-
T Consensus 54 ~~~~~~~rryagLyf~~~vd~tDnelayLe~IHlFVEvLd~fF~NVCELDlvFNFyKVy~i~DEm~l~GEi~Etsk~~vl 133 (143)
T KOG0935|consen 54 NFKIIYRRRYAGLYFCICVDVTDNELAYLEHIHLFVEVLDEFFHNVCELDLVFNFYKVYTIVDEMFLAGEIRETSKTKVL 133 (143)
T ss_pred eceEEEEEeeCCEEEEEEEecCCchHHHHHHHHHHHHHHHHHhccccceeeeeeeeeHHHHHHHHHHhhhhhhhhHHHHH
Confidence 34555667899999999999999999999999999999999999999999999999999999999999999998866543
No 12
>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.42 E-value=6.5e-07 Score=74.40 Aligned_cols=90 Identities=16% Similarity=0.155 Sum_probs=82.1
Q ss_pred CCEEEEEEEeCCEEEEEEEcCCCChhhHHHHHHHHHHHHhhhcCCCCHHHHHhhHHHHHHHHHhHhhCCcccccChHHHh
Q 017238 13 PTHYIFQIVRAGITFLACTQVEMPPLMGIEFLCRVADILSDYLGELNEDLIKDNFVIVYELLDEMIDNGFPLTTEPNILR 92 (375)
Q Consensus 13 ~~~~~~~~~~~~l~~v~v~~~~~n~~~~~~~L~~~~~vl~~y~~~l~e~~i~~n~~~i~~llde~id~G~p~~t~~~~lk 92 (375)
.+..++|+.+..||||.+.+...+-+.++++++-|.+.|...|.++.|-.+..|+..+..+|+|++.+|...+|+.|.+-
T Consensus 59 ~d~rlIYrhYATLYFvfvvD~sEsEL~iLDLIQvfVEtLDkCF~nVcELDliF~~~k~h~iL~EiV~GGmVlETn~neIv 138 (182)
T KOG0936|consen 59 SDNRLIYRHYATLYFVFVVDSSESELGILDLIQVFVETLDKCFENVCELDLIFNWQKVHAILAEIVMGGMVLETNMNEIV 138 (182)
T ss_pred ccceeehheeeeEEEEEEEcCCcchhHHHHHHHHHHHHHHHHHHhhhhhhheeeHHHHHHHHHHHHhCCeEEeccHHHHH
Confidence 46888999999999999999999999999999999999999999999999999999999999999999999999999877
Q ss_pred hhcCCCcchh
Q 017238 93 EMIAPPNIVS 102 (375)
Q Consensus 93 ~~i~~~s~~~ 102 (375)
.-+...+-.+
T Consensus 139 ~av~~~nkle 148 (182)
T KOG0936|consen 139 AAVDEQNKLE 148 (182)
T ss_pred HHHHHhchhh
Confidence 7666544333
No 13
>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.96 E-value=3e-05 Score=65.26 Aligned_cols=94 Identities=22% Similarity=0.291 Sum_probs=83.1
Q ss_pred eEEeCCEEEEEEEeCCEEEEEEEcCCCChhhHHHHHHHHHHHHhhhcCC-CCHHHHHhhHHHHHHHHHhHhhCCcccccC
Q 017238 9 VIASPTHYIFQIVRAGITFLACTQVEMPPLMGIEFLCRVADILSDYLGE-LNEDLIKDNFVIVYELLDEMIDNGFPLTTE 87 (375)
Q Consensus 9 v~~~~~~~~~~~~~~~l~~v~v~~~~~n~~~~~~~L~~~~~vl~~y~~~-l~e~~i~~n~~~i~~llde~id~G~p~~t~ 87 (375)
|...+++.++|...-+++|-.+-..+-|-++..+.|+.|.+.+.-.+.+ ..-..+.+|++.+...+|||+|.|...+|+
T Consensus 56 I~~ldg~~vvYk~~~Dl~fyv~G~~~ENEl~L~svL~~l~dal~llLr~nveKr~llEN~D~i~L~~DEiiD~GvILEtd 135 (175)
T KOG3343|consen 56 ILLLDGNTVVYKSVIDLHFYVVGSEEENELMLMSVLTCLFDALSLLLRKNVEKRELLENLDLIFLALDEIIDGGVILETD 135 (175)
T ss_pred eEEecCcEEEEEecccEEEEEecCcchhHHHHHHHHHHHHHHHHHHHHhChhHHHHHhhhccceeehhhhccCceEEecC
Confidence 6666888888788889999988888999999999999999999998875 777779999999999999999999999999
Q ss_pred hHHHhhhcCCCcchh
Q 017238 88 PNILREMIAPPNIVS 102 (375)
Q Consensus 88 ~~~lk~~i~~~s~~~ 102 (375)
++++-.-+..++...
T Consensus 136 p~~ia~rv~~~~~~~ 150 (175)
T KOG3343|consen 136 PNQIAQRVALRPTDE 150 (175)
T ss_pred HHHHHHHhccCCCCc
Confidence 999988887776544
No 14
>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=96.65 E-value=0.0053 Score=51.67 Aligned_cols=93 Identities=13% Similarity=0.143 Sum_probs=79.9
Q ss_pred ceEEeCCEEEEEEEeCCEEEEEEEcCCCChhhHHHHHHHHHHHHhhhcCCCC-HHHHHhhHHHHHHHHHhHhhCCccccc
Q 017238 8 PVIASPTHYIFQIVRAGITFLACTQVEMPPLMGIEFLCRVADILSDYLGELN-EDLIKDNFVIVYELLDEMIDNGFPLTT 86 (375)
Q Consensus 8 Pv~~~~~~~~~~~~~~~l~~v~v~~~~~n~~~~~~~L~~~~~vl~~y~~~l~-e~~i~~n~~~i~~llde~id~G~p~~t 86 (375)
-|....++-+.+.+..++.+..+..-+.|-.+.-+-+..|...|.-.++..+ +..+.+||+.|..++||.||.|....|
T Consensus 62 ~Il~f~d~lV~~k~~~dv~~yiv~~meeNE~~l~q~f~~ir~Al~li~k~~~dkr~v~enYDqivl~vdEtid~Gvilet 141 (187)
T COG5541 62 SILMFYDRLVMCKRLDDVLLYIVSPMEENEPFLGQVFDEIRAALILIVKTPTDKRNVWENYDQIVLLVDETIDEGVILET 141 (187)
T ss_pred ceeeEcceeeeeeeehhEEEEEecccccccHHHHHHHHHHHHHHHHHHcCCcchhhHHhhhceEEEeeehhcccceEeec
Confidence 4666667777778889988888888888888889999999999999998754 455999999999999999999999999
Q ss_pred ChHHHhhhcCCCcc
Q 017238 87 EPNILREMIAPPNI 100 (375)
Q Consensus 87 ~~~~lk~~i~~~s~ 100 (375)
+++.+.+-++.++.
T Consensus 142 ~s~~ia~rv~K~p~ 155 (187)
T COG5541 142 KSDEIADRVPKPPN 155 (187)
T ss_pred ChHHHHHhCCCCCC
Confidence 99999998887654
No 15
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=92.93 E-value=0.52 Score=41.73 Aligned_cols=82 Identities=12% Similarity=0.156 Sum_probs=68.3
Q ss_pred eCCEEEEEEEeCCEEEEEEEcCCCChhhHHHHHHHHHHHHhhhcCCCCH-HHHHhhHHHHHHHHHhHhhCCcccccChHH
Q 017238 12 SPTHYIFQIVRAGITFLACTQVEMPPLMGIEFLCRVADILSDYLGELNE-DLIKDNFVIVYELLDEMIDNGFPLTTEPNI 90 (375)
Q Consensus 12 ~~~~~~~~~~~~~l~~v~v~~~~~n~~~~~~~L~~~~~vl~~y~~~l~e-~~i~~n~~~i~~llde~id~G~p~~t~~~~ 90 (375)
.+...++ ...+++-|++||+..-|.++.-.||+.+.+.|.+.+..++. ..+....+.|.-+|+..++.|--.-.+.+.
T Consensus 102 ~~k~vvW-~~v~~l~ftLVce~hEN~lLa~~~L~~~~~~l~~~~~~l~~~~e~l~k~d~i~aiL~~fLP~GQLLFlN~~~ 180 (189)
T PF15001_consen 102 TPKIVVW-LGVGSLCFTLVCEPHENRLLAENTLRLFIRHLLEHLKILSQPSEVLLKSDRILAILHRFLPHGQLLFLNHRF 180 (189)
T ss_pred CCcEEEe-eccCCEEEEEEecCchhHHHHHHHHHHHHHHHHHHHHHhCcHHHhhhhHHHHHHHHHHhCCCCcEEEEcHHH
Confidence 3344444 88899999999999999999999999999999999976544 667788999999999999999877666666
Q ss_pred Hhhh
Q 017238 91 LREM 94 (375)
Q Consensus 91 lk~~ 94 (375)
+|.+
T Consensus 181 ~k~l 184 (189)
T PF15001_consen 181 VKQL 184 (189)
T ss_pred HHHH
Confidence 5543
No 16
>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=92.27 E-value=1 Score=34.08 Aligned_cols=48 Identities=21% Similarity=0.321 Sum_probs=41.7
Q ss_pred eEEeCCEEEEEEEeCCEEEEEEEcCCCChhhHHHHHHHHHHHHhhhcC
Q 017238 9 VIASPTHYIFQIVRAGITFLACTQVEMPPLMGIEFLCRVADILSDYLG 56 (375)
Q Consensus 9 v~~~~~~~~~~~~~~~l~~v~v~~~~~n~~~~~~~L~~~~~vl~~y~~ 56 (375)
.++.++..+.++..+++.++|+|+.+-+.-..+.||..+.+-...-++
T Consensus 18 s~~~~~~~fh~~~~~~i~~~citd~~~~~r~aF~fL~~i~~~F~~~~~ 65 (83)
T PF13774_consen 18 SYESGNYVFHYLVEDGIAYLCITDKSYPKRVAFAFLEEIKQEFIQTYG 65 (83)
T ss_dssp EEEETTEEEEEEEETTEEEEEEEETTS-HHHHHHHHHHHHHHHHHHCT
T ss_pred EEEECCEEEEEEEcCCeEEEEEEcCCCCcchHHHHHHHHHHHHHHHcC
Confidence 566788888777789999999999999999999999999999888877
No 17
>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=77.14 E-value=15 Score=27.94 Aligned_cols=43 Identities=19% Similarity=0.382 Sum_probs=29.8
Q ss_pred CceeeEEEEEeCCCCceeeEEEEcceeceeEeC-cEEEEEeCCCCCCC
Q 017238 261 KTIDSIILQFQLPPCILSADLTSNHGTVNVLSN-KICTWSIGRIPKDK 307 (375)
Q Consensus 261 ~~~~~v~I~ip~p~~~~~~~~~~~~G~~~~~~~-~~l~W~I~~~~~~~ 307 (375)
+.+-||.|+=++|-.. ++-.++-.. +--. +.|+|+|+++..|.
T Consensus 42 ~DcvnVviTqqLPce~---eFV~SdPet-tp~~D~kLVW~Ig~l~~G~ 85 (95)
T PF03504_consen 42 KDCVNVVITQQLPCEV---EFVRSDPET-TPTPDGKLVWKIGRLGQGE 85 (95)
T ss_pred cceeEEEEeecCCcce---EEEecCCcc-ccCCCCEEEEEeccccCCc
Confidence 4688899999999854 344444433 2222 88999999997664
No 18
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=76.53 E-value=22 Score=31.64 Aligned_cols=50 Identities=16% Similarity=0.228 Sum_probs=42.7
Q ss_pred eEEeCCEEEEEEEeCCEEEEEEEcCCCChhhHHHHHHHHHHHHhhhcCCC
Q 017238 9 VIASPTHYIFQIVRAGITFLACTQVEMPPLMGIEFLCRVADILSDYLGEL 58 (375)
Q Consensus 9 v~~~~~~~~~~~~~~~l~~v~v~~~~~n~~~~~~~L~~~~~vl~~y~~~l 58 (375)
.++++++.|.+...|++.|+|+++.+.-=-..+.||.++.+=+..-+|.-
T Consensus 45 tYs~d~y~Fh~l~~dg~tylcvadds~gR~ipfaFLe~Ik~~F~k~YG~~ 94 (217)
T KOG0859|consen 45 TYSCDGYTFHYLVEDGLTYLCVADDSAGRQIPFAFLERIKEDFKKRYGGG 94 (217)
T ss_pred EEecCCeEEEEEEeCCeEEEEEEeccccccccHHHHHHHHHHHHHHhccc
Confidence 57789999988888999999999888777778889999998888877753
No 19
>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=57.33 E-value=70 Score=26.20 Aligned_cols=45 Identities=9% Similarity=0.037 Sum_probs=38.3
Q ss_pred eEEeCCEEEEEEEeCCEEEEEEEcCCCChhhHHHHHHHHHHHHhh
Q 017238 9 VIASPTHYIFQIVRAGITFLACTQVEMPPLMGIEFLCRVADILSD 53 (375)
Q Consensus 9 v~~~~~~~~~~~~~~~l~~v~v~~~~~n~~~~~~~L~~~~~vl~~ 53 (375)
+..++++.+++.....+|+..++..+.|.-.++.+-.++..++.+
T Consensus 70 i~~Y~~~qvv~~~~~pl~it~ias~~aN~G~il~l~~~L~~~l~~ 114 (119)
T PF08923_consen 70 IAYYDSYQVVQFNKLPLYITFIASSNANTGLILSLEEELAPILNE 114 (119)
T ss_dssp EEEESSEEEEEEEETTEEEEEEEETTS-HHHHHHHHHHHHHHHHH
T ss_pred EEEeCCEEEEEEeCCCeEEEEEecCCCCHHHHHHhHHHHHHHHHH
Confidence 345588999999999999999999999999999888888888765
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=51.93 E-value=51 Score=22.63 Aligned_cols=32 Identities=13% Similarity=0.181 Sum_probs=26.9
Q ss_pred ccEEEEEEEeecCCCCceeeEEEEEeCCCCce
Q 017238 246 TCRISVMVGIRNDPGKTIDSIILQFQLPPCIL 277 (375)
Q Consensus 246 ~~~~ei~~~~~~~~~~~~~~v~I~ip~p~~~~ 277 (375)
+..+++++.++......+.+|.|+=++|.+..
T Consensus 11 Gd~v~Yti~v~N~g~~~a~~v~v~D~lP~g~~ 42 (53)
T TIGR01451 11 GDTITYTITVTNNGNVPATNVVVTDILPSGTT 42 (53)
T ss_pred CCEEEEEEEEEECCCCceEeEEEEEcCCCCCE
Confidence 57788888888766678999999999998764
No 21
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=49.83 E-value=64 Score=29.21 Aligned_cols=48 Identities=15% Similarity=0.353 Sum_probs=40.7
Q ss_pred EEeCCEEEEEEEeCCEEEEEEEcCCCChhhHHHHHHHHHHHHhhhcCC
Q 017238 10 IASPTHYIFQIVRAGITFLACTQVEMPPLMGIEFLCRVADILSDYLGE 57 (375)
Q Consensus 10 ~~~~~~~~~~~~~~~l~~v~v~~~~~n~~~~~~~L~~~~~vl~~y~~~ 57 (375)
++.|.+.|.++..+++.+.++|+.+-+--+.+.+|+.+.+=+..-++.
T Consensus 54 ietg~f~fHfli~~~Vcylvicd~~yP~kLAF~YLedL~~EF~~~~~~ 101 (216)
T KOG0862|consen 54 IETGPFVFHFLIESGVCYLVICDKSYPRKLAFSYLEDLAQEFDKSYGK 101 (216)
T ss_pred cccCCeEEEEEecCCEEEEEEecCCCcHHHHHHHHHHHHHHHHHhccc
Confidence 344667787788889999999999999999999999999888777764
No 22
>PRK06764 hypothetical protein; Provisional
Probab=49.50 E-value=56 Score=24.98 Aligned_cols=48 Identities=29% Similarity=0.349 Sum_probs=27.9
Q ss_pred CccEEEEEEE-CceeccccEEeEEEeecCCCcccccEEEEEecccEEEc
Q 017238 327 FPTFQVEFRI-MGVALSGLQIDKLDLQNVPNRLYKGFRAVTRAGEYEVR 374 (375)
Q Consensus 327 ~~~i~v~F~i-~~~s~SGl~V~~l~v~~~~~~~~k~vky~t~sg~y~ir 374 (375)
+..|.|.-.. +.|.+||-+|+-++=..+.....|+---..+-|.|.||
T Consensus 41 fn~i~v~mn~~e~y~lsgrsidilsgdkeaiqlnkyti~f~kpg~yvir 89 (105)
T PRK06764 41 FNAIDVSMNINELYVLSGRSIDVLSGDKEAIQLNKYTIRFSKPGKYVIR 89 (105)
T ss_pred cceEEEEEeccceEEEcCceeeeecCChhheEeeeeEEEecCCccEEEE
Confidence 4566676654 56889996666554322333344432222446899887
No 23
>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=38.38 E-value=1.5e+02 Score=29.67 Aligned_cols=44 Identities=14% Similarity=0.066 Sum_probs=31.9
Q ss_pred EEeCCEEEEEEEeCCEEEEEEEcCCCChhhHHHHHHHHHHHHhh
Q 017238 10 IASPTHYIFQIVRAGITFLACTQVEMPPLMGIEFLCRVADILSD 53 (375)
Q Consensus 10 ~~~~~~~~~~~~~~~l~~v~v~~~~~n~~~~~~~L~~~~~vl~~ 53 (375)
+..|++.|+...++-||+||+++...++.....-|+.+...|-.
T Consensus 58 i~~~~~~ivfl~r~pl~lv~vS~~~e~~~~l~~qL~~ly~qils 101 (415)
T PF03164_consen 58 IRAGDHRIVFLNRGPLILVAVSKTGESESQLRKQLDYLYSQILS 101 (415)
T ss_pred EEeCCEEEEEEecCCEEEEEEcCCcCCHHHHHHHHHHHHHHHHH
Confidence 45688999989999999999998877766555545444444443
No 24
>KOG0647 consensus mRNA export protein (contains WD40 repeats) [RNA processing and modification]
Probab=30.77 E-value=85 Score=30.07 Aligned_cols=104 Identities=18% Similarity=0.284 Sum_probs=65.3
Q ss_pred EEeEEEEEccCCcEEEEEEEEEEEEEEeeCCCCeeEEEecCCc----c------cccceeccee-ecCCCCCCceEEEeC
Q 017238 146 VEEMDAIINRDGVLVKCEIYGEVQVNCLLSGLPDLTLSFANPS----I------LHDVRFHPCV-RFRPWESHQILSFVP 214 (375)
Q Consensus 146 ~E~v~~~~~~~G~i~~~~v~G~i~~~~~LsG~P~~~l~ln~~~----~------l~d~~fH~cV-~~~~f~~~~~i~f~P 214 (375)
+-.|.|.-|++|. .-..|.|++.+..-..++|.-.+.|.-.. . ..++.|||-- .+..-.+|..++|=.
T Consensus 201 ~R~va~f~d~~~~-alGsiEGrv~iq~id~~~~~~nFtFkCHR~~~~~~~~VYaVNsi~FhP~hgtlvTaGsDGtf~FWD 279 (347)
T KOG0647|consen 201 TRCVACFQDKDGF-ALGSIEGRVAIQYIDDPNPKDNFTFKCHRSTNSVNDDVYAVNSIAFHPVHGTLVTAGSDGTFSFWD 279 (347)
T ss_pred eeEEEEEecCCce-EeeeecceEEEEecCCCCccCceeEEEeccCCCCCCceEEecceEeecccceEEEecCCceEEEec
Confidence 4467777888888 77889999999998999987777774221 1 3457888821 122234556666666
Q ss_pred CCCcEEEEEEEecCCCCCCEEEEEEEEEcCCccEEEEEEEee
Q 017238 215 PDGQFKLMSYRVKKLKSTPIYVKPQLTSDAGTCRISVMVGIR 256 (375)
Q Consensus 215 PdG~F~Lm~Y~~~~~~~~P~~v~~~~~~~~~~~~~ei~~~~~ 256 (375)
-|.+-.|..|..- ..|++. |.+. .++.=|-|.+.+.
T Consensus 280 kdar~kLk~s~~~---~qpItc-c~fn--~~G~ifaYA~gYD 315 (347)
T KOG0647|consen 280 KDARTKLKTSETH---PQPITC-CSFN--RNGSIFAYALGYD 315 (347)
T ss_pred chhhhhhhccCcC---CCccce-eEec--CCCCEEEEEeecc
Confidence 6666566665532 236655 3333 3356677777665
No 25
>PF01345 DUF11: Domain of unknown function DUF11; InterPro: IPR001434 This group of sequences is represented by a 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 (Streptococcus faecalis), and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydia trachomatis outer membrane proteins. In C. trachomatis, three cysteine-rich proteins (also believed to be lipoproteins), MOMP, OMP6 and OMP3, make up the extracellular matrix of the outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. They are thought to be involved in porin formation and, as these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism.; GO: 0005727 extrachromosomal circular DNA
Probab=24.54 E-value=1.8e+02 Score=21.09 Aligned_cols=32 Identities=9% Similarity=0.196 Sum_probs=26.9
Q ss_pred ccEEEEEEEeecCCCCceeeEEEEEeCCCCce
Q 017238 246 TCRISVMVGIRNDPGKTIDSIILQFQLPPCIL 277 (375)
Q Consensus 246 ~~~~ei~~~~~~~~~~~~~~v~I~ip~p~~~~ 277 (375)
+..++|++.+.......+.+|.|.=++|.+..
T Consensus 40 Gd~v~ytitvtN~G~~~a~nv~v~D~lp~g~~ 71 (76)
T PF01345_consen 40 GDTVTYTITVTNTGPAPATNVVVTDTLPAGLT 71 (76)
T ss_pred CCEEEEEEEEEECCCCeeEeEEEEEcCCCCCE
Confidence 57899999888766678999999999998653
No 26
>PF10633 NPCBM_assoc: NPCBM-associated, NEW3 domain of alpha-galactosidase; InterPro: IPR018905 This domain has been named NEW3, but its function is not known. It is found on proteins which are bacterial galactosidases [].; PDB: 1EUT_A 2BZD_A 1WCQ_C 2BER_A 1W8O_A 1EUU_A 1W8N_A.
Probab=23.36 E-value=1.5e+02 Score=21.77 Aligned_cols=31 Identities=16% Similarity=0.281 Sum_probs=19.0
Q ss_pred cEEEEEEEeecCCCCceeeEEEEEeCCCCce
Q 017238 247 CRISVMVGIRNDPGKTIDSIILQFQLPPCIL 277 (375)
Q Consensus 247 ~~~ei~~~~~~~~~~~~~~v~I~ip~p~~~~ 277 (375)
..+.+++.+.......+.++.+++-+|.+|.
T Consensus 5 ~~~~~~~tv~N~g~~~~~~v~~~l~~P~GW~ 35 (78)
T PF10633_consen 5 ETVTVTLTVTNTGTAPLTNVSLSLSLPEGWT 35 (78)
T ss_dssp EEEEEEEEEE--SSS-BSS-EEEEE--TTSE
T ss_pred CEEEEEEEEEECCCCceeeEEEEEeCCCCcc
Confidence 4566666666554567899999999999997
No 27
>KOG1766 consensus Enhancer of rudimentary [General function prediction only]
Probab=22.79 E-value=96 Score=24.23 Aligned_cols=42 Identities=14% Similarity=0.266 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHhhhcCCC--CHHHHHhhHHHHHHHHHhHhhCC
Q 017238 40 GIEFLCRVADILSDYLGEL--NEDLIKDNFVIVYELLDEMIDNG 81 (375)
Q Consensus 40 ~~~~L~~~~~vl~~y~~~l--~e~~i~~n~~~i~~llde~id~G 81 (375)
+-+.|..+.++.+++++.. +...|......+|+.||.+.|-.
T Consensus 25 v~e~megiCk~yEe~Lkk~nPs~~~ITYDIsqlfeFiD~L~DlS 68 (104)
T KOG1766|consen 25 VTECMEGICKMYEEHLKKKNPSAPPITYDISQLFEFIDDLADLS 68 (104)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCcceeHHHHHHHHHHHhhhh
Confidence 5678889999999999864 66678899999999999988754
No 28
>PF02334 RTP: Replication terminator protein; InterPro: IPR003432 The bacterial replication terminator protein (RTP) plays a role in the termination of DNA replication by impeding replication fork movement. Two RTP dimers bind to the two inverted repeat regions at the termination site.; GO: 0003677 DNA binding, 0006274 DNA replication termination; PDB: 2DPU_A 2DPD_A 1F4K_A 1J0R_B 2EFW_F 2DQR_B 1BM9_B.
Probab=20.07 E-value=1.7e+02 Score=23.73 Aligned_cols=34 Identities=29% Similarity=0.460 Sum_probs=23.5
Q ss_pred HHHHHhhhcCCCCHHHHHhhHHHHHHHHHhHhhCCcc
Q 017238 47 VADILSDYLGELNEDLIKDNFVIVYELLDEMIDNGFP 83 (375)
Q Consensus 47 ~~~vl~~y~~~l~e~~i~~n~~~i~~llde~id~G~p 83 (375)
+.+.|++=|.++. -+-|..+||..|+|+++.|+-
T Consensus 37 ~Ld~lr~EFk~~G---y~P~hsEvYraLHeL~~dGil 70 (122)
T PF02334_consen 37 LLDELRSEFKPLG---YRPNHSEVYRALHELVDDGIL 70 (122)
T ss_dssp HHHHHHHHHTTTT-------HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHhhhcC---CCCCHHHHHHHHHHHHhhhHH
Confidence 4456666666555 556889999999999999984
Done!