Query 020859
Match_columns 320
No_of_seqs 155 out of 1195
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 05:43:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020859.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020859hhsearch_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-79 7.4E-84 553.8 28.3 314 4-320 1-341 (446)
2 KOG0937 Adaptor complexes medi 100.0 3.8E-68 8.2E-73 500.8 30.0 315 5-320 1-317 (424)
3 KOG2740 Clathrin-associated pr 100.0 5.1E-61 1.1E-65 439.0 23.8 288 4-306 1-303 (418)
4 PF00928 Adap_comp_sub: Adapto 100.0 8E-37 1.7E-41 280.8 18.9 155 159-320 1-156 (262)
5 KOG2635 Medium subunit of clat 100.0 7.9E-28 1.7E-32 225.7 25.9 296 3-320 1-417 (512)
6 PF01217 Clat_adaptor_s: Clath 100.0 8.6E-29 1.9E-33 207.4 17.4 135 4-141 1-138 (141)
7 COG5030 APS2 Clathrin adaptor 99.9 7.1E-22 1.5E-26 159.1 13.9 133 4-139 1-136 (152)
8 KOG2677 Stoned B synaptic vesi 99.9 1.1E-23 2.3E-28 204.9 3.7 154 166-320 582-753 (922)
9 KOG0934 Clathrin adaptor compl 99.8 9.1E-21 2E-25 152.5 7.9 132 4-138 1-135 (145)
10 KOG3343 Vesicle coat complex C 99.8 1.7E-19 3.7E-24 148.5 13.2 139 4-144 8-149 (175)
11 KOG0935 Clathrin adaptor compl 99.8 3.1E-19 6.8E-24 140.2 11.6 134 4-139 1-137 (143)
12 KOG0936 Clathrin adaptor compl 99.8 2.1E-18 4.6E-23 140.9 13.3 157 4-163 1-166 (182)
13 COG5541 RET3 Vesicle coat comp 99.5 2.2E-13 4.7E-18 112.1 9.0 139 4-144 7-156 (187)
14 PF15001 AP-5_subunit_s1: AP-5 96.8 0.077 1.7E-06 46.3 14.9 80 57-136 103-183 (189)
15 PF03164 Mon1: Trafficking pro 96.3 0.042 9.1E-07 54.1 11.4 88 6-98 12-103 (415)
16 PF10291 muHD: Muniscin C-term 95.4 1.3 2.8E-05 40.8 16.6 131 173-319 3-151 (257)
17 KOG0997 Uncharacterized conser 92.9 0.91 2E-05 44.9 10.1 75 6-84 118-195 (523)
18 COG5122 TRS23 Transport protei 92.6 2.8 6.1E-05 33.5 10.6 90 4-100 2-108 (134)
19 PF04099 Sybindin: Sybindin-li 91.7 5 0.00011 33.4 12.0 94 5-99 1-116 (142)
20 KOG0859 Synaptobrevin/VAMP-lik 91.5 6 0.00013 34.8 12.4 89 8-100 4-93 (217)
21 PF08923 MAPKK1_Int: Mitogen-a 91.5 3.3 7.1E-05 33.6 10.4 91 5-96 17-114 (119)
22 PF13774 Longin: Regulated-SNA 91.4 1.5 3.3E-05 32.7 7.9 49 51-99 17-65 (83)
23 PF09201 SRX: SRX; InterPro: 87.7 12 0.00026 31.0 10.8 73 4-76 1-86 (148)
24 KOG0781 Signal recognition par 86.7 9.8 0.00021 38.1 11.4 114 4-120 1-117 (587)
25 KOG3369 Transport protein part 79.4 40 0.00087 29.2 10.9 46 52-99 125-171 (199)
26 KOG3368 Transport protein part 66.6 73 0.0016 26.3 10.3 86 3-92 1-102 (140)
27 KOG0862 Synaptobrevin/VAMP-lik 60.9 1.2E+02 0.0025 27.2 10.1 49 52-100 53-101 (216)
28 PF05228 CHASE4: CHASE4 domain 29.0 3.1E+02 0.0066 22.2 7.5 20 5-24 50-71 (161)
29 KOG0647 mRNA export protein (c 28.5 1.4E+02 0.0031 28.2 5.7 113 179-301 202-315 (347)
30 PF07151 DUF1391: Protein of u 27.6 69 0.0015 21.1 2.4 17 258-274 16-32 (49)
31 COG3322 Predicted periplasmic 25.4 78 0.0017 29.8 3.4 36 5-40 104-141 (295)
32 PF00235 Profilin: Profilin; 25.3 3.3E+02 0.0072 21.3 9.5 87 5-94 16-121 (121)
33 KOG1766 Enhancer of rudimentar 25.1 1E+02 0.0022 23.9 3.4 42 83-124 25-68 (104)
No 1
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=3.4e-79 Score=553.77 Aligned_cols=314 Identities=38% Similarity=0.685 Sum_probs=289.6
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCChhHHHHHHHHhhccCCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCHHHH
Q 020859 4 AVSALFLLDIKGRVLVWRDYRGDVSAKQAERFFTKLIEKDGDAQSQDPVVYDNGVSYLFIQHSNVYLMTASRQNCNAASL 83 (320)
Q Consensus 4 MI~~i~Il~~~G~~ll~k~y~~~~~~~~~~~f~~~i~~~~~~~~~~~pi~~~~~~~~v~~~~~~l~~v~~~~~~~n~l~~ 83 (320)
||+++||+|.+|++++.|.||+|..++..+.|+.+++..... .+|+..+++..|+|.+.++||+++++.+|.|.+.+
T Consensus 1 misglfi~n~rGevlink~fr~dlkrs~~diFRv~vi~n~d~---r~PV~~igsttf~~~r~~nl~lvaitksN~Nva~v 77 (446)
T KOG0938|consen 1 MISGLFIYNLRGEVLINKTFRDDLKRSIVDIFRVQVINNLDV---RSPVLTIGSTTFHHIRSSNLWLVAITKSNANVAAV 77 (446)
T ss_pred CcceEEEEeccCcEEEehhhhhhhhhhHHHHHHHhhhhcccc---CCCeeEecceeEEEEeeccEEEEEEecCCCchhhH
Confidence 899999999999999999999999999999999999987543 58999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcccchhHHhhhHHHHHHHHHHHhcCCeeeeechhhhhHhhcccccccccc----C-----CC---
Q 020859 84 LFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDAYRMEVT----Q-----RP--- 151 (320)
Q Consensus 84 ~~~L~~~~~~l~~y~~~l~e~~I~~Nf~~vy~lLDEiid~G~p~~t~~~~L~~~i~~~~~~~~~~----~-----~~--- 151 (320)
++||..+..++..|||+.+|+.|++||.+|||+||||+|+|+||+|++++|+.+|..+++..+-. + ++
T Consensus 78 ~eFl~kl~avm~aYfgk~~Eeaiknnf~lI~ElLDemld~G~pqnte~~al~~~is~~~Vrs~g~~ls~k~s~~sq~~~~ 157 (446)
T KOG0938|consen 78 FEFLYKLDAVMNAYFGKDREEAIKNNFVLIYELLDEMLDFGIPQNTEPNALKAQISQKGVRSMGGVLSSKSSPTSQATEL 157 (446)
T ss_pred HHHHHHHHHHHHHHhcccchhhhhhceEeHHHHHHHHHhcCCCccCChhHHHhhhhhhhhhccccccCCcCCCCcccccc
Confidence 99999999999999999999999999999999999999999999999999999999887765421 1 11
Q ss_pred -CCcccCCccCccCCCccccceEEEEEEEeEeEEEcCCCcEEEEEEEEEEEEEEEeCCCCeEEEEeccchhhhhccC---
Q 020859 152 -PMAVTNAVSWRSEGIQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQGR--- 227 (320)
Q Consensus 152 -~~~~~~~~~wR~~~~~~~~nei~vdv~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~~--- 227 (320)
+++.+++++||++|++|+|||+|+||+|++|.+++++|++++++|.|.|.|+++|||||+|++||||.+.+.+..+
T Consensus 158 ~ssqv~G~i~WRr~Gi~ykknevfldvvErvNlLmS~~GnVLrs~VsG~V~mk~~LSGmPeckfGlNDkl~~e~kq~esk 237 (446)
T KOG0938|consen 158 RSSQVTGKIGWRREGIKYKKNEVFLDVVERVNLLMSSDGNVLRSDVSGTVDMKTHLSGMPECKFGLNDKLGMESKQSESK 237 (446)
T ss_pred cccccccccccccccceeccceeEeEehheeeeEEcCCCCEEEeecccEEEEEEeccCCcccccccCcccceeecccccc
Confidence 1345678999999999999999999999999999999999999999999999999999999999999987773210
Q ss_pred ----------CCCCceeecccCccccccccccccCCceEEEeCCCCceEEEEEEeeCCCCCcEEEEEEEEEcCceEEEEE
Q 020859 228 ----------STKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLNTQVKPLIWVEAQVERHSRSRVEIL 297 (320)
Q Consensus 228 ----------~~~~~~~~l~d~~fH~cV~~~~f~~~~~l~F~PPdg~f~Lm~Y~~~~~~~~P~~v~~~~~~~~~~~~e~~ 297 (320)
.+....+.|+||.||+||++++|+++++|+|+||||+|+||+||+..+..+||+|.|.+++.+.++++|.
T Consensus 238 s~~~n~~~~sks~~g~v~leDc~FHqCV~L~kFn~eh~IsFvPPDGe~ELMkYr~~enInlPFrV~PiV~el~r~kie~r 317 (446)
T KOG0938|consen 238 SDFGNKNFPSKSGKGSVLLEDCTFHQCVRLDKFNSEHIISFVPPDGEFELMKYRVTENINLPFRVTPIVTELGRTKIEYR 317 (446)
T ss_pred ccccccCCCcccCCceEEeeccchheeeccccccccceEEEeCCCCceEeEeeeeccCcccceEeeeheecccceeEEEE
Confidence 1234558999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeecCCCceece-eeEEeeeCC
Q 020859 298 VKARSQFKERRCSD-INGICIICT 320 (320)
Q Consensus 298 ~~l~~~~~~~~~~~-~~~~~p~p~ 320 (320)
+.++++|++++.|. ++++||+|.
T Consensus 318 i~iks~f~~kl~a~~v~~rIPvP~ 341 (446)
T KOG0938|consen 318 ITIKSLFPPKLLAKDVVVRIPVPP 341 (446)
T ss_pred EEEeccCCchhhhcceEEEecCCC
Confidence 99999999999885 889999995
No 2
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=3.8e-68 Score=500.81 Aligned_cols=315 Identities=57% Similarity=0.984 Sum_probs=290.9
Q ss_pred eeEEEEEcCCCCEEEEEccCCCCChhHHHHHHHHhhccCCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCHHHHH
Q 020859 5 VSALFLLDIKGRVLVWRDYRGDVSAKQAERFFTKLIEKDGDAQSQDPVVYDNGVSYLFIQHSNVYLMTASRQNCNAASLL 84 (320)
Q Consensus 5 I~~i~Il~~~G~~ll~k~y~~~~~~~~~~~f~~~i~~~~~~~~~~~pi~~~~~~~~v~~~~~~l~~v~~~~~~~n~l~~~ 84 (320)
++|+||+|.+|++|++|.||++.+.+..+.|++++.... .....+|++..+|+.|+|.+.+++|++++++.|.+++.++
T Consensus 1 ~sa~fild~~G~~lisr~yr~dv~~s~~~~F~~~l~~~e-~~~~~~p~l~~~g~~~~~ik~s~lylv~~~~~n~~a~~v~ 79 (424)
T KOG0937|consen 1 ASAVFILDHKGEVLISRDYRGDVPMSSTEKFFRKLFEKE-EGDESPPFLVHDGSRFIHIKHSNLYLVAGTRPNVSAALVL 79 (424)
T ss_pred CceEEEEcCCCcEeEeecccccCChhhhhhHHHHHhhhc-ccCCCCCeEEeCCceEEEEeecceEEEEEeccCCCHHHHH
Confidence 589999999999999999999999999999998766543 2235689999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhcccchhHHhhhHHHHHHHHHHHhcCCeeeeechhhhhHhhccccccccccC-CCCCcccCCccCcc
Q 020859 85 FFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDAYRMEVTQ-RPPMAVTNAVSWRS 163 (320)
Q Consensus 85 ~~L~~~~~~l~~y~~~l~e~~I~~Nf~~vy~lLDEiid~G~p~~t~~~~L~~~i~~~~~~~~~~~-~~~~~~~~~~~wR~ 163 (320)
+||+++++++.+||+.+.|+.++.||+++||+|||++||||||.|+.+.|++++..++......+ ++|.+.+++++||+
T Consensus 80 ~~l~~~~~v~~~y~~~l~e~si~~n~vlvyElLde~mDFGypQ~t~s~iL~~yi~~~~~~l~~~~~~~p~avtnavsWrs 159 (424)
T KOG0937|consen 80 SFLYAVADVFGDYLSELEEESIRDNFVLVYELLDEVMDFGYPQTTDSEILKNYITQKANRLQDAQPRPPLAVTNAVSWRS 159 (424)
T ss_pred HHHHHHHHHHHHHhccCCccceecchHHHHHHHHHHhccCCcccchHHHHHHHhcccccceeecCCCCCcccccceeecc
Confidence 99999999999999999999999999999999999999999999999999999999976654332 56888899999999
Q ss_pred CCCccccceEEEEEEEeEeEEEcCCCcEEEEEEEEEEEEEEEeCCCCeEEEEeccchhhhhccCCCCCceeecccCcccc
Q 020859 164 EGIQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQGRSTKGKAIDLDDIKFHQ 243 (320)
Q Consensus 164 ~~~~~~~nei~vdv~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~l~d~~fH~ 243 (320)
.|++|+|||+|+||+|+++++++++|.++.++|.|+|+|||+|+|||+++|+||+....+..+..+++..+.++|++||+
T Consensus 160 ~gi~~~KnevflDViE~Vs~l~~~~G~vl~s~i~G~I~~k~~LsGmPelrl~ln~~~~~~~~~~~~~s~~v~ledi~fh~ 239 (424)
T KOG0937|consen 160 EGIYYGKNEVFLDVIESVSLLYDSNGIVLLSEIVGTIKLKCYLSGMPELRLGLNDKVLFDKQGPRSKSKGVELEDIKFHE 239 (424)
T ss_pred cccccccceEEEEhhhhhhHhhhcCCcEEEeeeeeEEEEEEEcCCCceeeeecCcccccccccccccCcceEeeecccce
Confidence 99999999999999999999999999999999999999999999999999999999988877755566789999999999
Q ss_pred ccccccccCCceEEEeCCCCceEEEEEEeeCCCCCcEEEEEEEEEcCceEEEEEEEEeecCCCceece-eeEEeeeCC
Q 020859 244 CVRLARFENDRTISFIPPDGSFDLMTYRLNTQVKPLIWVEAQVERHSRSRVEILVKARSQFKERRCSD-INGICIICT 320 (320)
Q Consensus 244 cV~~~~f~~~~~l~F~PPdg~f~Lm~Y~~~~~~~~P~~v~~~~~~~~~~~~e~~~~l~~~~~~~~~~~-~~~~~p~p~ 320 (320)
||++++|+.+|+|+|+||||+|+||+||.+....|++.+....+.++..++++.++++++|+++..|+ +.|.+|+|.
T Consensus 240 ~v~l~~fd~dr~i~FiPPdGeF~Lm~Y~ls~~vkPli~~~~~~~~~~~~ri~i~~K~~~~fk~~~~a~~v~I~iP~P~ 317 (424)
T KOG0937|consen 240 CVRLSRFDNDRTISFIPPDGEFELMRYRLSTHVKPLIWFYQLIEEHSRSRIEVMVKLREQFKSRSSANNVEICIPVPD 317 (424)
T ss_pred eechhhccCCceEEecCCCCceEEEEEEecCCCCCeEEeeeeeeeccceeEEEEEechhhcCCccccceEEEEeeCCC
Confidence 99999999999999999999999999999988888888766666777889999999999999999886 789999994
No 3
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=5.1e-61 Score=439.04 Aligned_cols=288 Identities=33% Similarity=0.631 Sum_probs=256.8
Q ss_pred ceeEEEEEcCCCCEEEEEccCC-CCChhHHHHHHHHhhccCCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCHHH
Q 020859 4 AVSALFLLDIKGRVLVWRDYRG-DVSAKQAERFFTKLIEKDGDAQSQDPVVYDNGVSYLFIQHSNVYLMTASRQNCNAAS 82 (320)
Q Consensus 4 MI~~i~Il~~~G~~ll~k~y~~-~~~~~~~~~f~~~i~~~~~~~~~~~pi~~~~~~~~v~~~~~~l~~v~~~~~~~n~l~ 82 (320)
||.+||+.|.+|+++++|.+++ ..+|+.++.|+......... .+.+|++..+.++++-+-+++++|++++..+..||+
T Consensus 1 mi~siflidtsg~l~lek~~~g~t~~rsic~~f~e~~~~~~~~-e~~ppvi~~p~hylfsv~~~~i~~~~~st~e~pPL~ 79 (418)
T KOG2740|consen 1 MILSIFLIDTSGDLLLEKHLKGSTVVRSICDYFFEDQSSDDDL-EHVPPVISTPHHYLFSVYRDLIFFCAVSTVETPPLM 79 (418)
T ss_pred CeeEEEEEcCCchhhhhHhhCCceeeeehHHHHHHhhhhcccc-ccCCceecCCceeeeeeeccCcEEEEEEeccCCChh
Confidence 8999999999999999999994 56678888888887765433 356788888888888888999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcccchhHHhhhHHHHHHHHHHHhcCCeeeeechhhhhHhhcccccccccc----------CCCC
Q 020859 83 LLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDAYRMEVT----------QRPP 152 (320)
Q Consensus 83 ~~~~L~~~~~~l~~y~~~l~e~~I~~Nf~~vy~lLDEiid~G~p~~t~~~~L~~~i~~~~~~~~~~----------~~~~ 152 (320)
+++||+++++++++|||+++|.+|++|++.||++||||+|+|+|..||+|.|+++|+.++...+.. ...|
T Consensus 80 ~iefL~rv~dv~~eyFg~~s~~~Ik~N~~vv~ell~emiDnGfpl~tE~NiLke~i~pps~l~~~~~svTg~~n~~~~lP 159 (418)
T KOG2740|consen 80 VIEFLHRVVDVLLEYFGGLSESKIKDNVVVVYELLDEMIDNGFPLVTEPNILKELIPPPSFLSKKFNSVTGNSNVSDTLP 159 (418)
T ss_pred HHHHHHHHHHHHHHHhcccCHhHhhcceeeHHHHHHHHHHcCCCcccChhHHHhhcCChHHHHHHHhhhhccccccccCC
Confidence 999999999999999999999999999999999999999999999999999999999998887421 1456
Q ss_pred CcccCCccCccCCCccccceEEEEEEEeEeEEEcCCCcEEEEEEEEEEEEEEEeCCCCeEEEEeccchhhhhccCCCCCc
Q 020859 153 MAVTNAVSWRSEGIQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQGRSTKGK 232 (320)
Q Consensus 153 ~~~~~~~~wR~~~~~~~~nei~vdv~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~ 232 (320)
+++.+.+|||+.+.+|++||.||||+|+++|+++++|+.+.++|.|.|.|+|.|+|||++.|.|+.+.
T Consensus 160 tg~~s~VPWR~~~~Ky~nNE~yvdvlEeidai~~k~gslv~~eI~g~vd~~~qLsgmPdltlsl~np~------------ 227 (418)
T KOG2740|consen 160 TGALSNVPWRTAGVKYTNNEAYVDVLEEIDAIVDKKGSLVFGEIQGIVDVCSQLSGMPDLTLSLNNPR------------ 227 (418)
T ss_pred CcccccccccccCcccccchhhhhhhheeheEecCCCCEEEEEEEEEEEEEEeecCCCceEEEccCcc------------
Confidence 66777899999999999999999999999999999999999999999999999999999999998763
Q ss_pred eeecccCccccccccccccCCceEEEeCCCCceEEEEEEeeCC--CCCcEEEEEEEEEcCc--eEEEEEEEEeecCCC
Q 020859 233 AIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLNTQ--VKPLIWVEAQVERHSR--SRVEILVKARSQFKE 306 (320)
Q Consensus 233 ~~~l~d~~fH~cV~~~~f~~~~~l~F~PPdg~f~Lm~Y~~~~~--~~~P~~v~~~~~~~~~--~~~e~~~~l~~~~~~ 306 (320)
.|+|++||+||++.+|++++.|+|+||||+|+||+||++.+ ...|..++++++..+. .|++++++.+....+
T Consensus 228 --~L~dvsfHpcVr~krwe~~~~lsFIPPDGkFrLlsy~v~~~~~v~~pvyv~~~i~l~~~~~~ri~~tvg~~~~~gK 303 (418)
T KOG2740|consen 228 --LLGDVSFHPCVRYKRWESHSVLSFIPPDGKFRLLSYRVDAQNQVAIPVYVKNSISLDSNHQGRISLTVGPKKKMGK 303 (418)
T ss_pred --ccCCcccccceeecccccccceEEcCCCCcEEEEEEEEehhhccccceEEeeeeccCCCceEEEEEeccccccccc
Confidence 58999999999999999999999999999999999999864 4889999999987654 366666655555544
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=8e-37 Score=280.78 Aligned_cols=155 Identities=39% Similarity=0.755 Sum_probs=129.3
Q ss_pred ccCccCCCccccceEEEEEEEeEeEEEcCCCcEEEEEEEEEEEEEEEeCCCCeEEEEeccchhhhhccCCCCCceeeccc
Q 020859 159 VSWRSEGIQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQGRSTKGKAIDLDD 238 (320)
Q Consensus 159 ~~wR~~~~~~~~nei~vdv~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~l~d 238 (320)
+|||+.+.+|++|||||||.|+++++++++|.++.++|.|+|.|+++|+|+|+|+|+||++... ...++.++|
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 6899999999999999999999999999999999999999999999999999999999987433 235678999
Q ss_pred CccccccccccccCCceEEEeCCCCceEEEEEEeeCCCCCcEEEEEEEEEcCceEEEEEEEEeecCCCce-eceeeEEee
Q 020859 239 IKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLNTQVKPLIWVEAQVERHSRSRVEILVKARSQFKERR-CSDINGICI 317 (320)
Q Consensus 239 ~~fH~cV~~~~f~~~~~l~F~PPdg~f~Lm~Y~~~~~~~~P~~v~~~~~~~~~~~~e~~~~l~~~~~~~~-~~~~~~~~p 317 (320)
++||+||++++|++++.|+|+||||+|+||+||++.+..+||.++|++.+.+++++++.++++++++... ..++.+.+|
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 9999999999999999999999999999999999988999999999999877789999999999998865 557889999
Q ss_pred eCC
Q 020859 318 ICT 320 (320)
Q Consensus 318 ~p~ 320 (320)
+|.
T Consensus 154 lP~ 156 (262)
T PF00928_consen 154 LPP 156 (262)
T ss_dssp --T
T ss_pred cCC
Confidence 993
No 5
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.96 E-value=7.9e-28 Score=225.66 Aligned_cols=296 Identities=16% Similarity=0.258 Sum_probs=239.8
Q ss_pred cceeEEEEEcCCCCEEEEEccCCCCChh----HHHHHHHHhhccCCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCC
Q 020859 3 GAVSALFLLDIKGRVLVWRDYRGDVSAK----QAERFFTKLIEKDGDAQSQDPVVYDNGVSYLFIQHSNVYLMTASRQNC 78 (320)
Q Consensus 3 ~MI~~i~Il~~~G~~ll~k~y~~~~~~~----~~~~f~~~i~~~~~~~~~~~pi~~~~~~~~v~~~~~~l~~v~~~~~~~ 78 (320)
||+-|..|++..|+.+++|+|+ +++|. .+.+|.+.+-.. +++.+++.+.++|||+..+++|++.+|..+.
T Consensus 1 Mvvlaa~i~t~~Gk~ivsRqf~-~Msr~RIEgLl~aFpkLv~~~-----~qhT~vEt~~VRYVYqP~d~lY~vLITtk~S 74 (512)
T KOG2635|consen 1 MVVLAASINTKTGKAIVSRQFR-EMSRSRIEGLLAAFPKLVSAG-----KQHTFVETDSVRYVYQPLDNLYIVLITTKQS 74 (512)
T ss_pred CeEEEEEEeecCCceeeehHhH-hhhHHHHHHHHHHhHHhhccC-----CCccEEecccEEEEEEecccEEEEEEecccc
Confidence 5778999999999999999999 67764 456677766532 4689999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHHHHHhcccchhHHhhhHHHHHHHHHHHhcCCeeeeechhhhhHhhccccccccccC---------
Q 020859 79 NAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDAYRMEVTQ--------- 149 (320)
Q Consensus 79 n~l~~~~~L~~~~~~l~~y~~~l~e~~I~~Nf~~vy~lLDEiid~G~p~~t~~~~L~~~i~~~~~~~~~~~--------- 149 (320)
|.+-.++.|+.|.+++..||..++|+.|.+|-..+...+||++..||-...+..+++.|..++++++++..
T Consensus 75 NIleDl~TL~Lfskvipey~~slde~eI~~~~FelifAFDEivsLGyre~v~laQikty~eMdSHEEKi~e~v~~nke~e 154 (512)
T KOG2635|consen 75 NILEDLETLRLFSKVIPEYCSSLDEKEILENAFELIFAFDEIVSLGYRENVNLAQIKTYLEMDSHEEKIHELVMRNKERE 154 (512)
T ss_pred chhhHHHHHHHHHHhchhhhhhhhHHHHHHhhhhhhhccchhhhhcccccccHHHhhhhhccccHHHHHHHHHHHhhhHH
Confidence 99999999999999999999999999999998888889999999999999999999999999999876310
Q ss_pred ------------------------------------------------------CCC---C-cccCCccCc---------
Q 020859 150 ------------------------------------------------------RPP---M-AVTNAVSWR--------- 162 (320)
Q Consensus 150 ------------------------------------------------------~~~---~-~~~~~~~wR--------- 162 (320)
..+ + +.....|-+
T Consensus 155 a~q~mkrKaKElqr~r~ea~rrgg~~~~~~~~~~s~g~~~~s~~~~~~~~~~~~~~~~~~sa~~~~s~pak~mklG~k~~ 234 (512)
T KOG2635|consen 155 AKQEMKRKAKELQRARKEAERRGGSLNPGFDAIGSSGYSSVSTTNAINRVESIAQKPKQQSAAKASSAPAKAMKLGKKTK 234 (512)
T ss_pred HHHHHHHHHHHHHHHHHhhhccccccCCCccccccccccCCcccchhhccccccccccccccccCCCCCchhhhhccccc
Confidence 000 0 000000000
Q ss_pred --------------------------------cCCCccccceEEEEEEEeEeEEEcCCCcEEEEEEEEEEEEEEEeCCCC
Q 020859 163 --------------------------------SEGIQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMP 210 (320)
Q Consensus 163 --------------------------------~~~~~~~~nei~vdv~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P 210 (320)
+....-.++-+++.+.|++++.+++||.+-+.++.|.+.++.--...-
T Consensus 235 ~s~~~~d~Lk~ege~ia~~~s~~g~~s~aap~~~~p~v~~e~v~i~ieEkln~~~~RDGgi~s~E~qG~lsLrI~d~e~~ 314 (512)
T KOG2635|consen 235 NSDTFVDKLKGEGERIAGASSAIGSASSAAPPPTAPDVPEESVHIVIEEKLNVRLSRDGGIKSGEVQGTLSLRIKDEEYG 314 (512)
T ss_pred chhhHHHHhhccccccccccccccccccCCCCCCCCCCccceEEEEEeeeEeEEEcccCCccceeeeeeEEEEEcccccc
Confidence 000111234499999999999999999999999999999999888888
Q ss_pred eEEEEeccchhhhhccCCCCCceeecccCccccccccccccCCceEEEeCCCCce------EEEEEEeeCC--CCCcEEE
Q 020859 211 ECKLGLNDRILLEAQGRSTKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSF------DLMTYRLNTQ--VKPLIWV 282 (320)
Q Consensus 211 ~~~l~ln~~~~~~~~~~~~~~~~~~l~d~~fH~cV~~~~f~~~~~l~F~PPdg~f------~Lm~Y~~~~~--~~~P~~v 282 (320)
.+.|.|++.. . .=.++++||.+|++.|.++..|...+|+..| .|++||.... ...|+.+
T Consensus 315 ~i~lkl~n~~----------~---~g~q~ktHPNlDK~~f~s~s~iglk~~~K~FPvn~~VGvLkWR~~~~des~iPlTi 381 (512)
T KOG2635|consen 315 DIELKLANGR----------D---KGTQLKTHPNLDKKVFLSSSLIGLKRPEKPFPVNSDVGVLKWRMVDEDESEIPLTI 381 (512)
T ss_pred ceEEEEcCCC----------C---cceeeeeCCCcchhhhccccccccccCCCCCCcCCcceEEEEeecccccccCceEE
Confidence 8999987631 0 1247899999999999999999999999988 5999998763 4899999
Q ss_pred EEEEEEcCceEEEEEEEEeecCCCc-eeceeeEEeeeCC
Q 020859 283 EAQVERHSRSRVEILVKARSQFKER-RCSDINGICIICT 320 (320)
Q Consensus 283 ~~~~~~~~~~~~e~~~~l~~~~~~~-~~~~~~~~~p~p~ 320 (320)
+||.++.+.+ +++.|++.. ... -..++.+.+|+|+
T Consensus 382 ncWPSes~~g-~dV~iEYe~--~~~~eL~dV~i~iPlP~ 417 (512)
T KOG2635|consen 382 NCWPSESGNG-YDVNIEYEA--VLECELNDVIITIPLPA 417 (512)
T ss_pred EeccccCCCC-eEEEEEEee--hhcccccceEEEeeccc
Confidence 9999988765 555555554 112 3457899999996
No 6
>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=99.96 E-value=8.6e-29 Score=207.39 Aligned_cols=135 Identities=27% Similarity=0.510 Sum_probs=116.8
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCChh---HHHHHHHHhhccCCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCH
Q 020859 4 AVSALFLLDIKGRVLVWRDYRGDVSAK---QAERFFTKLIEKDGDAQSQDPVVYDNGVSYLFIQHSNVYLMTASRQNCNA 80 (320)
Q Consensus 4 MI~~i~Il~~~G~~ll~k~y~~~~~~~---~~~~f~~~i~~~~~~~~~~~pi~~~~~~~~v~~~~~~l~~v~~~~~~~n~ 80 (320)
||+|++|+|++|+++++|||++..... ..+++.+.+..+++ ..+|++.++++.++|++.+++||+++++.++||
T Consensus 1 MI~~i~i~n~~G~~i~~k~y~~~~~~~~~~~~~~~~~~~~~~~~---~~~~i~~~~~~~~vy~~~~dl~~~~v~~~~eNe 77 (141)
T PF01217_consen 1 MIKAILILNSQGKRILSKYYRDVSEEERQKLFEKFIKKKSSRNS---KQSPIFEHDNYRIVYKRYSDLYFVVVGDENENE 77 (141)
T ss_dssp SEEEEEEEETTSEEEEEEESSTSTSHHHHHHHHHHHHHHHTSSS---SSTSEEEETTEEEEEEEETTEEEEEEESSTSBH
T ss_pred CEEEEEEEcCCCCEEEehhcCCccHHHHHHHHHHHHHHHHhccc---ccceeeecccceeeeEeeccEEEEEEeecccch
Confidence 999999999999999999997644432 33444444444432 358999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhcccchhHHhhhHHHHHHHHHHHhcCCeeeeechhhhhHhhccc
Q 020859 81 ASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTD 141 (320)
Q Consensus 81 l~~~~~L~~~~~~l~~y~~~l~e~~I~~Nf~~vy~lLDEiid~G~p~~t~~~~L~~~i~~~ 141 (320)
++++++|++++++|+.||++++|..|++||+.+|++||||+|+|+|++|+++.|.+++.+.
T Consensus 78 l~~~e~l~~~v~~l~~~~~~v~e~~i~~N~~~v~~~LDEiid~G~i~etd~~~I~~~v~~~ 138 (141)
T PF01217_consen 78 LLLLEFLHRLVEVLDDYFGNVSEKDILENFDLVYLILDEIIDGGIILETDPNVILKRVTMQ 138 (141)
T ss_dssp HHHHHHHHHHHHHHHHHHSS-SHHHHHHTHHHHHHHHHHHEETTEES--THHHHHHHHHHC
T ss_pred HHHHHHHHHhhhhhhhhhccccHHHHHHCHHHHHHHHHHHHhCCEEEECCHHHHHHHHHHh
Confidence 9999999999999999999999999999999999999999999999999999999998754
No 7
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=99.88 E-value=7.1e-22 Score=159.09 Aligned_cols=133 Identities=17% Similarity=0.274 Sum_probs=119.5
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCC--h-hHHHHHHHHhhccCCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCH
Q 020859 4 AVSALFLLDIKGRVLVWRDYRGDVS--A-KQAERFFTKLIEKDGDAQSQDPVVYDNGVSYLFIQHSNVYLMTASRQNCNA 80 (320)
Q Consensus 4 MI~~i~Il~~~G~~ll~k~y~~~~~--~-~~~~~f~~~i~~~~~~~~~~~pi~~~~~~~~v~~~~~~l~~v~~~~~~~n~ 80 (320)
||++++|+|++|++++.|||.+... + ..+....+.+.+++. +.+.+++..+..++|+++++|||+++.+.++|+
T Consensus 1 ~i~~vli~nrqgk~RL~K~yt~~~~~e~~kli~~i~~lIs~R~~---ke~N~~e~k~~kiVYrrYA~LyF~f~Vd~~dnE 77 (152)
T COG5030 1 MIKFVLIFNRQGKPRLVKWYTPVSDPEQAKLIADIYELISARKP---KESNFIEGKNEKIVYRRYATLYFVFGVDNDDNE 77 (152)
T ss_pred CeEEEEEEcCCCceeeeEeeccCCcHHHHHHHHHHHHHHHcCCc---hhcccccccCcEEEeeecCcEEEEEEEcCCCCc
Confidence 8999999999999999999986433 2 256778888888753 468899999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhcccchhHHhhhHHHHHHHHHHHhcCCeeeeechhhhhHhhc
Q 020859 81 ASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIK 139 (320)
Q Consensus 81 l~~~~~L~~~~~~l~~y~~~l~e~~I~~Nf~~vy~lLDEiid~G~p~~t~~~~L~~~i~ 139 (320)
+.+++++|.|+++|+.||+++||.++..||..+|.+||||+-+|..++++++.+.+.+.
T Consensus 78 l~iL~lIh~FVE~lDr~FgnVCELdlIFNF~kv~~ILdE~i~gG~i~Es~~~~vl~~v~ 136 (152)
T COG5030 78 LIILELIHNFVEILDRFFGNVCELDLIFNFQKVYAILDEMILGGEIIESSKNEVLEHVY 136 (152)
T ss_pred chHHHHHHHHHHHHHHHhccceeeEeEeeHHHHHHHHHHHHhCCeeeecCHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999987765553
No 8
>KOG2677 consensus Stoned B synaptic vesicle biogenesis protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.88 E-value=1.1e-23 Score=204.89 Aligned_cols=154 Identities=28% Similarity=0.469 Sum_probs=130.9
Q ss_pred CccccceEEEEEEEeEeEEEcCCCcEEEEEEEEEEEEEEEeCCCCeEEEEeccchhhhhcc-------CCCCCceeeccc
Q 020859 166 IQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQG-------RSTKGKAIDLDD 238 (320)
Q Consensus 166 ~~~~~nei~vdv~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~-------~~~~~~~~~l~d 238 (320)
..|..+||.|||.++.+++++++|+++...|..+|.|.|||+|.|+|.|+|||..+.++.- +.....||+|.+
T Consensus 582 ~nY~e~EI~v~~~Defsg~V~Keg~~~~~~v~tri~cL~FlsG~~ec~lgLND~~~kg~Eiv~rkDimp~~t~kwI~~~~ 661 (922)
T KOG2677|consen 582 SNYLEEEITVDVRDEFSGIVSKEGQILQHHVLTRIHCLSFLSGLAECRLGLNDILVKGNEIVLRKDIMPTTTTKWIKLHE 661 (922)
T ss_pred cccccceeEEEEEeccceeecccchhhhhhhhhhhhhhhhccCCceeEeecchhhhcccceeEeccccccccccceeeee
Confidence 4799999999999999999999999999999999999999999999999999998755431 234679999999
Q ss_pred CccccccccccccCCceEEEeCCCC-ceEEEEEEeeCC-CCCcEEEEEEEEEcCceEEEEEEEE--eecCCCc-------
Q 020859 239 IKFHQCVRLARFENDRTISFIPPDG-SFDLMTYRLNTQ-VKPLIWVEAQVERHSRSRVEILVKA--RSQFKER------- 307 (320)
Q Consensus 239 ~~fH~cV~~~~f~~~~~l~F~PPdg-~f~Lm~Y~~~~~-~~~P~~v~~~~~~~~~~~~e~~~~l--~~~~~~~------- 307 (320)
|.||.|||.++|+++|+|.|.|||| +|+|||||+..+ ..+||.++..+...| ..+|+..-+ .+.|.++
T Consensus 662 ~~FH~cVn~~eF~~srVI~F~PlDaCrFElMRFrt~~~~~~lpftlks~~~V~G-a~VEvq~~~~mat~~qr~rd~~~~v 740 (922)
T KOG2677|consen 662 CRFHGCVNEDEFHNSRVILFNPLDACRFELMRFRTVFAEKTLPFTLKSATSVNG-AEVEVQSWLRMATGFQRNRDPLTQV 740 (922)
T ss_pred eeeecccchhhccccceEEecCcccceeeeeeeeeecCCCcCceeeeeeeeecc-ceeehHHHHHHHhhhhhccCccccC
Confidence 9999999999999999999999999 999999999765 489999998887764 456665433 3333332
Q ss_pred eeceeeEEeeeCC
Q 020859 308 RCSDINGICIICT 320 (320)
Q Consensus 308 ~~~~~~~~~p~p~ 320 (320)
-|.++.|+.|+|+
T Consensus 741 pCenI~IrfPVPs 753 (922)
T KOG2677|consen 741 PCENIMIRFPVPS 753 (922)
T ss_pred cccceeEeccCcH
Confidence 3567889999994
No 9
>KOG0934 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.83 E-value=9.1e-21 Score=152.54 Aligned_cols=132 Identities=18% Similarity=0.264 Sum_probs=116.4
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCC--hh-HHHHHHHHhhccCCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCH
Q 020859 4 AVSALFLLDIKGRVLVWRDYRGDVS--AK-QAERFFTKLIEKDGDAQSQDPVVYDNGVSYLFIQHSNVYLMTASRQNCNA 80 (320)
Q Consensus 4 MI~~i~Il~~~G~~ll~k~y~~~~~--~~-~~~~f~~~i~~~~~~~~~~~pi~~~~~~~~v~~~~~~l~~v~~~~~~~n~ 80 (320)
||++++..+++|+++++|||..... |. ......+.+++++. ..+.+++.++...||+++++|||++....++|+
T Consensus 1 mi~f~LlvsrQGk~rL~k~y~~~~~~er~~i~re~i~~~Lar~p---k~csfie~kd~kvVyrryasl~f~~~v~~~dNE 77 (145)
T KOG0934|consen 1 MIKFFLLVSRQGKTRLQKWYEALSIKERKKIERELIKSVLARKP---KMCSFIEYKDEKVVYRRYASLFFCVGVEDNDNE 77 (145)
T ss_pred CeEEEEEEeccCceehhHHHhhhcHHHHHHHHHHHHHHHHhCCc---ccccchhccCceehhhhhhhEEEEEEEecCCch
Confidence 8999999999999999999986433 22 34566777777653 468999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhcccchhHHhhhHHHHHHHHHHHhcCCeeeeechhhhhHhh
Q 020859 81 ASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFI 138 (320)
Q Consensus 81 l~~~~~L~~~~~~l~~y~~~l~e~~I~~Nf~~vy~lLDEiid~G~p~~t~~~~L~~~i 138 (320)
+.+++++|+++++|+.|||++||.+|..||..+|.+|||++-.|..+++..+....-+
T Consensus 78 L~~LE~IH~~vE~lDkYFg~VCELDiiFNfekay~ILde~~~~g~~~e~~k~~~~~~i 135 (145)
T KOG0934|consen 78 LAILEFIHNYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEIQETSKNDVLKAI 135 (145)
T ss_pred hhHHHHHHHHHHHHHHHhccceeeEEEEehHhHHHHHHHHhcCcchHhhhcccHHHHH
Confidence 9999999999999999999999999999999999999999999999999887543333
No 10
>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.82 E-value=1.7e-19 Score=148.50 Aligned_cols=139 Identities=17% Similarity=0.312 Sum_probs=126.9
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCChh--HHHHHHHHhhccCCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCHH
Q 020859 4 AVSALFLLDIKGRVLVWRDYRGDVSAK--QAERFFTKLIEKDGDAQSQDPVVYDNGVSYLFIQHSNVYLMTASRQNCNAA 81 (320)
Q Consensus 4 MI~~i~Il~~~G~~ll~k~y~~~~~~~--~~~~f~~~i~~~~~~~~~~~pi~~~~~~~~v~~~~~~l~~v~~~~~~~n~l 81 (320)
.++|++|+|++|++++.|||.++.+.. ...+|.+.+.++... +...|...+|..++|+..-||+|..+...++|++
T Consensus 8 ~vk~iliLD~~G~Ri~aKYY~~~~~s~vkeqkaFEK~lF~KT~k--t~~eI~~ldg~~vvYk~~~Dl~fyv~G~~~ENEl 85 (175)
T KOG3343|consen 8 TVKAILILDSDGKRILAKYYDDPHPSTVKEQKAFEKNLFSKTSK--TESEILLLDGNTVVYKSVIDLHFYVVGSEEENEL 85 (175)
T ss_pred hhheEEEEcCCCCEeeeeecCCCcchhHHHHHHHHHHHhccccc--ccceeEEecCcEEEEEecccEEEEEecCcchhHH
Confidence 368999999999999999999988763 456899988877543 5688999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhcc-cchhHHhhhHHHHHHHHHHHhcCCeeeeechhhhhHhhcccccc
Q 020859 82 SLLFFLHRVVDVFKHYFEE-LEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDAYR 144 (320)
Q Consensus 82 ~~~~~L~~~~~~l~~y~~~-l~e~~I~~Nf~~vy~lLDEiid~G~p~~t~~~~L~~~i~~~~~~ 144 (320)
+..+.|+.+.+.+...+++ ++...+.+|++.+...+|||+|+|.+++||++++..++..++..
T Consensus 86 ~L~svL~~l~dal~llLr~nveKr~llEN~D~i~L~~DEiiD~GvILEtdp~~ia~rv~~~~~~ 149 (175)
T KOG3343|consen 86 MLMSVLTCLFDALSLLLRKNVEKRELLENLDLIFLALDEIIDGGVILETDPNQIAQRVALRPTD 149 (175)
T ss_pred HHHHHHHHHHHHHHHHHHhChhHHHHHhhhccceeehhhhccCceEEecCHHHHHHHhccCCCC
Confidence 9999999999999999996 99999999999999999999999999999999999999877654
No 11
>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.81 E-value=3.1e-19 Score=140.21 Aligned_cols=134 Identities=19% Similarity=0.208 Sum_probs=112.7
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCC--h-hHHHHHHHHhhccCCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCH
Q 020859 4 AVSALFLLDIKGRVLVWRDYRGDVS--A-KQAERFFTKLIEKDGDAQSQDPVVYDNGVSYLFIQHSNVYLMTASRQNCNA 80 (320)
Q Consensus 4 MI~~i~Il~~~G~~ll~k~y~~~~~--~-~~~~~f~~~i~~~~~~~~~~~pi~~~~~~~~v~~~~~~l~~v~~~~~~~n~ 80 (320)
||.+|+|.|+.|+.+++|||.+... + ...+...+.+..++.. .+.-+........+++++++|||+...+.-+|+
T Consensus 1 mi~FILiqNr~Gk~RLak~yv~~dd~ek~~~~~~vh~lvs~Rd~K--~~~~~~~~~~~~~~~rryagLyf~~~vd~tDne 78 (143)
T KOG0935|consen 1 MIRFILIQNRAGKTRLAKWYVQFDDDEKQKLIEEVHALVTVRDAK--HTNFVEFRNFKIIYRRRYAGLYFCICVDVTDNE 78 (143)
T ss_pred CeEEEEEEccccceeheeeeeccCchHHHHHHHHHHHHHhhccch--hhhheeeeeceEEEEEeeCCEEEEEEEecCCch
Confidence 8999999999999999999975333 2 2456677777766432 334455555556666799999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhcccchhHHhhhHHHHHHHHHHHhcCCeeeeechhhhhHhhc
Q 020859 81 ASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIK 139 (320)
Q Consensus 81 l~~~~~L~~~~~~l~~y~~~l~e~~I~~Nf~~vy~lLDEiid~G~p~~t~~~~L~~~i~ 139 (320)
+..++.+|.|+++|+.||+++||.++..||-.||.++|||+-+|.+++|++..+-+.+.
T Consensus 79 layLe~IHlFVEvLd~fF~NVCELDlvFNFyKVy~i~DEm~l~GEi~Etsk~~vlerl~ 137 (143)
T KOG0935|consen 79 LAYLEHIHLFVEVLDEFFHNVCELDLVFNFYKVYTIVDEMFLAGEIRETSKTKVLERLL 137 (143)
T ss_pred HHHHHHHHHHHHHHHHHhccccceeeeeeeeeHHHHHHHHHHhhhhhhhhHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999987766553
No 12
>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.79 E-value=2.1e-18 Score=140.89 Aligned_cols=157 Identities=15% Similarity=0.139 Sum_probs=126.4
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCC---hhHHHHHHHHhhccCCCCCCCCCEEEe------CCEEEEEEEeCCEEEEEEe
Q 020859 4 AVSALFLLDIKGRVLVWRDYRGDVS---AKQAERFFTKLIEKDGDAQSQDPVVYD------NGVSYLFIQHSNVYLMTAS 74 (320)
Q Consensus 4 MI~~i~Il~~~G~~ll~k~y~~~~~---~~~~~~f~~~i~~~~~~~~~~~pi~~~------~~~~~v~~~~~~l~~v~~~ 74 (320)
||+|++|+|.+|++++.|+|.+-.. +..++..+..+.++++. .+.+++. .+...+|+.+..|||+.+.
T Consensus 1 MI~AvlifNn~gkPRL~KFY~p~~~~~Qq~lir~vf~lvs~R~~n---~~nFLe~~~l~g~~d~rlIYrhYATLYFvfvv 77 (182)
T KOG0936|consen 1 MIKAVLIFNNKGKPRLVKFYTPVDEEKQQQLIREVFHLVSKRPDN---VCNFLEGNSLIGGSDNRLIYRHYATLYFVFVV 77 (182)
T ss_pred CeeEEEEecCCCCcceeeecCcCChHHHHHHHHHHHHHHHcCCch---HhhhhccccccCCccceeehheeeeEEEEEEE
Confidence 9999999999999999999986332 23567777888777632 3555542 3689999999999999999
Q ss_pred cCCCCHHHHHHHHHHHHHHHHHHhcccchhHHhhhHHHHHHHHHHHhcCCeeeeechhhhhHhhccccccccccCCCCCc
Q 020859 75 RQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDAYRMEVTQRPPMA 154 (320)
Q Consensus 75 ~~~~n~l~~~~~L~~~~~~l~~y~~~l~e~~I~~Nf~~vy~lLDEiid~G~p~~t~~~~L~~~i~~~~~~~~~~~~~~~~ 154 (320)
++.++++.++++++-|++.|+..|.+++|.++..|++.++.+|+|++.+|...+|+.+.+...+....-..+.....+.+
T Consensus 78 D~sEsEL~iLDLIQvfVEtLDkCF~nVcELDliF~~~k~h~iL~EiV~GGmVlETn~neIv~av~~~nkleks~~~~~~~ 157 (182)
T KOG0936|consen 78 DSSESELGILDLIQVFVETLDKCFENVCELDLIFNWQKVHAILAEIVMGGMVLETNMNEIVAAVDEQNKLEKSEDGLIGA 157 (182)
T ss_pred cCCcchhHHHHHHHHHHHHHHHHHHhhhhhhheeeHHHHHHHHHHHHhCCeEEeccHHHHHHHHHHhchhhhccCCcccC
Confidence 99999999999999999999999999999999999999999999999999999999998887776544333322222223
Q ss_pred ccCCccCcc
Q 020859 155 VTNAVSWRS 163 (320)
Q Consensus 155 ~~~~~~wR~ 163 (320)
.+++..|+.
T Consensus 158 p~~~~~~~~ 166 (182)
T KOG0936|consen 158 PTRAVFAVK 166 (182)
T ss_pred chhhhhhhh
Confidence 334445553
No 13
>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=99.47 E-value=2.2e-13 Score=112.09 Aligned_cols=139 Identities=17% Similarity=0.225 Sum_probs=120.4
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCChh----------HHHHHHHHhhccCCCCCCCCCEEEeCCEEEEEEEeCCEEEEEE
Q 020859 4 AVSALFLLDIKGRVLVWRDYRGDVSAK----------QAERFFTKLIEKDGDAQSQDPVVYDNGVSYLFIQHSNVYLMTA 73 (320)
Q Consensus 4 MI~~i~Il~~~G~~ll~k~y~~~~~~~----------~~~~f~~~i~~~~~~~~~~~pi~~~~~~~~v~~~~~~l~~v~~ 73 (320)
-+.|++|+|++|++++.|||.+...+. -..+|.+.+..+... +...|...++..+++.+..++.|+.+
T Consensus 7 ~v~a~LilDsqGeriy~kyy~pph~~eg~~~vFnsvkkekefek~l~eKt~k--~~~~Il~f~d~lV~~k~~~dv~~yiv 84 (187)
T COG5541 7 DVEALLILDSQGERIYRKYYQPPHRSEGHQLVFNSVKKEKEFEKKLAEKTAK--DRESILMFYDRLVMCKRLDDVLLYIV 84 (187)
T ss_pred eeeeeEEecCCccchhhhhcCCcccccccchhhcchhHHHHHHHHHHHHhhc--CccceeeEcceeeeeeeehhEEEEEe
Confidence 368999999999999999998755431 235677777665332 45789999999999999999999999
Q ss_pred ecCCCCHHHHHHHHHHHHHHHHHHhcc-cchhHHhhhHHHHHHHHHHHhcCCeeeeechhhhhHhhcccccc
Q 020859 74 SRQNCNAASLLFFLHRVVDVFKHYFEE-LEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDAYR 144 (320)
Q Consensus 74 ~~~~~n~l~~~~~L~~~~~~l~~y~~~-l~e~~I~~Nf~~vy~lLDEiid~G~p~~t~~~~L~~~i~~~~~~ 144 (320)
..-++|+.+..+.+..|...|...++. .++..+.+|||.+..+.||.||.|.+.+|+++.+.+.++.++..
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 999999999999999999999999997 66677999999999999999999999999999999999886654
No 14
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=96.81 E-value=0.077 Score=46.33 Aligned_cols=80 Identities=6% Similarity=0.052 Sum_probs=70.8
Q ss_pred CEEEEEEEeCCEEEEEEecCCCCHHHHHHHHHHHHHHHHHHhcccch-hHHhhhHHHHHHHHHHHhcCCeeeeechhhhh
Q 020859 57 GVSYLFIQHSNVYLMTASRQNCNAASLLFFLHRVVDVFKHYFEELEE-ESLRDNFVVVYELLDEMMDFGYPQYTEANILS 135 (320)
Q Consensus 57 ~~~~v~~~~~~l~~v~~~~~~~n~l~~~~~L~~~~~~l~~y~~~l~e-~~I~~Nf~~vy~lLDEiid~G~p~~t~~~~L~ 135 (320)
...+++....++-|..+++..+|-+++-.+|+.++..|.+.++.++. ..+...-|.|..+|+..++.|.-.-.+.+.++
T Consensus 103 ~k~vvW~~v~~l~ftLVce~hEN~lLa~~~L~~~~~~l~~~~~~l~~~~e~l~k~d~i~aiL~~fLP~GQLLFlN~~~~k 182 (189)
T PF15001_consen 103 PKIVVWLGVGSLCFTLVCEPHENRLLAENTLRLFIRHLLEHLKILSQPSEVLLKSDRILAILHRFLPHGQLLFLNHRFVK 182 (189)
T ss_pred CcEEEeeccCCEEEEEEecCchhHHHHHHHHHHHHHHHHHHHHHhCcHHHhhhhHHHHHHHHHHhCCCCcEEEEcHHHHH
Confidence 36889999999999999999999999999999999999999976443 66778999999999999999998888876554
Q ss_pred H
Q 020859 136 E 136 (320)
Q Consensus 136 ~ 136 (320)
.
T Consensus 183 ~ 183 (189)
T PF15001_consen 183 Q 183 (189)
T ss_pred H
Confidence 4
No 15
>PF03164 Mon1: Trafficking protein Mon1; InterPro: IPR004353 Members of this family have been called SAND proteins [] although these proteins do not contain a SAND domain. In Saccharomyces cerevisiae a protein complex of Mon1 and Ccz1 functions with the small GTPase Ypt7 to mediate vesicle trafficking to the vacuole [, ]. The Mon1/Ccz1 complex is conserved in eukaryotic evolution and members of this family (previously known as DUF254) are distant homologues to domains of known structure that assemble into cargo vesicle adapter (AP) complexes [, ].
Probab=96.31 E-value=0.042 Score=54.10 Aligned_cols=88 Identities=10% Similarity=0.136 Sum_probs=58.9
Q ss_pred eEEEEEcCCCCEEEEEccCCCCCh----hHHHHHHHHhhccCCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCHH
Q 020859 6 SALFLLDIKGRVLVWRDYRGDVSA----KQAERFFTKLIEKDGDAQSQDPVVYDNGVSYLFIQHSNVYLMTASRQNCNAA 81 (320)
Q Consensus 6 ~~i~Il~~~G~~ll~k~y~~~~~~----~~~~~f~~~i~~~~~~~~~~~pi~~~~~~~~v~~~~~~l~~v~~~~~~~n~l 81 (320)
+.+||++..||++++|+ .++..- +.+.++..-+.... +.---+..++..+++..++.||+||+++..+++.
T Consensus 12 kh~fIlS~AGKPIysr~-G~e~~l~~~~g~~~aiiS~~~~~~----d~l~~i~~~~~~ivfl~r~pl~lv~vS~~~e~~~ 86 (415)
T PF03164_consen 12 KHFFILSSAGKPIYSRY-GDEDKLSSLMGVIQAIISFFQSNG----DELRSIRAGDHRIVFLNRGPLILVAVSKTGESES 86 (415)
T ss_pred CeEEEECCCCceeEEec-CChHHHHHHHHHHHHHHHHHHhCC----CcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCHH
Confidence 57999999999999988 332221 12233332222221 1123456789999999999999999999999877
Q ss_pred HHHHHHHHHHHHHHHHh
Q 020859 82 SLLFFLHRVVDVFKHYF 98 (320)
Q Consensus 82 ~~~~~L~~~~~~l~~y~ 98 (320)
.+..-|+.+...+-..+
T Consensus 87 ~l~~qL~~ly~qils~l 103 (415)
T PF03164_consen 87 QLRKQLDYLYSQILSIL 103 (415)
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 76666666555555443
No 16
>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=95.45 E-value=1.3 Score=40.78 Aligned_cols=131 Identities=11% Similarity=0.120 Sum_probs=70.6
Q ss_pred EEEEEEEeEeEEEcCCCcEEEEEEEEEEEEEEEeCC------CCeEEEEeccchhhhhccCCCCCceeecccCccccccc
Q 020859 173 VFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSG------MPECKLGLNDRILLEAQGRSTKGKAIDLDDIKFHQCVR 246 (320)
Q Consensus 173 i~vdv~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG------~P~~~l~ln~~~~~~~~~~~~~~~~~~l~d~~fH~cV~ 246 (320)
+-..|.|.|||.+. +|.+..+.|.|.|.+.---.- .+.+.+.|+.... |+.+.-.+..=
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 45679999999985 578888999999987533221 3467788865532 22222111110
Q ss_pred cccccCCceEEEeCC--CCce--EEEEEEeeCC----CCCcEEEEEEEEEcCceEEEEEEEEeecC---CCc-eeceeeE
Q 020859 247 LARFENDRTISFIPP--DGSF--DLMTYRLNTQ----VKPLIWVEAQVERHSRSRVEILVKARSQF---KER-RCSDING 314 (320)
Q Consensus 247 ~~~f~~~~~l~F~PP--dg~f--~Lm~Y~~~~~----~~~P~~v~~~~~~~~~~~~e~~~~l~~~~---~~~-~~~~~~~ 314 (320)
...-..+....|.++ .... ..++|++... ..+|+.+.|.-+-. +.+.++.|.++.+- ... ...|+++
T Consensus 68 ~~~~~~~~~f~~n~~~l~~~~~~~alKYqv~~~~~~~~~~Pl~l~~~Wk~e-~~~tsl~l~Y~~Np~~~~~~~~L~nv~~ 146 (257)
T PF10291_consen 68 SSSSQSDGEFWLNMSALTSHLPKQALKYQVHSDPSNLSSVPLILKPVWKCE-PSQTSLILDYKLNPDAFASPVPLENVVF 146 (257)
T ss_dssp --EEEETTEEEE-TTTTBT-E-EEEEEEEEES--------SEEEEEEEEE--SSEEEEEEEEEE-TTT--E-EEEEEEEE
T ss_pred ecCCCCCCcEEEehHHhhhhhhhceEEEEEeccccccCCCCeEEEeEEEeC-CceEEEEEEEEeChhhccccceeeeEEE
Confidence 001112234555554 2333 5799999763 57899998877654 33455555555443 332 3456778
Q ss_pred EeeeC
Q 020859 315 ICIIC 319 (320)
Q Consensus 315 ~~p~p 319 (320)
..++.
T Consensus 147 ~v~l~ 151 (257)
T PF10291_consen 147 SVPLD 151 (257)
T ss_dssp EEEB-
T ss_pred EEEcC
Confidence 77765
No 17
>KOG0997 consensus Uncharacterized conserved protein Sand [Function unknown]
Probab=92.87 E-value=0.91 Score=44.92 Aligned_cols=75 Identities=20% Similarity=0.259 Sum_probs=49.8
Q ss_pred eEEEEEcCCCCEEEEEccCCCCCh---hHHHHHHHHhhccCCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCHHH
Q 020859 6 SALFLLDIKGRVLVWRDYRGDVSA---KQAERFFTKLIEKDGDAQSQDPVVYDNGVSYLFIQHSNVYLMTASRQNCNAAS 82 (320)
Q Consensus 6 ~~i~Il~~~G~~ll~k~y~~~~~~---~~~~~f~~~i~~~~~~~~~~~pi~~~~~~~~v~~~~~~l~~v~~~~~~~n~l~ 82 (320)
+.+||+.+.|+++++|+=..+... ++..+...-+-... ..-..+..+|..+++.+++.|++||++..+..+..
T Consensus 118 khifilseaGKPiyS~~gs~e~l~stmGv~~alISf~q~~~----~~i~si~a~g~k~vfl~kspl~LvA~s~t~~Sa~q 193 (523)
T KOG0997|consen 118 KHIFILSEAGKPIYSRHGSDEALSSTMGVMQALISFFQVSG----LAITSIHAFGNKLVFLQKSPLLLVAVSRTSQSAAQ 193 (523)
T ss_pred ceEEEEecCCCceeeecCcHHHHHHHHHHHHHHHHHHhhCC----ceEEEEEecCceEEEEecCcEEEEEEcccccCHHH
Confidence 469999999999999985533221 12222222221111 12345678899999999999999999997776544
Q ss_pred HH
Q 020859 83 LL 84 (320)
Q Consensus 83 ~~ 84 (320)
..
T Consensus 194 L~ 195 (523)
T KOG0997|consen 194 LL 195 (523)
T ss_pred HH
Confidence 33
No 18
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=92.56 E-value=2.8 Score=33.46 Aligned_cols=90 Identities=17% Similarity=0.348 Sum_probs=55.8
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCCh----------hH---HHHHHHHhhccCCCCCCCCC--EEEeCC-EEEEEEEeCC
Q 020859 4 AVSALFLLDIKGRVLVWRDYRGDVSA----------KQ---AERFFTKLIEKDGDAQSQDP--VVYDNG-VSYLFIQHSN 67 (320)
Q Consensus 4 MI~~i~Il~~~G~~ll~k~y~~~~~~----------~~---~~~f~~~i~~~~~~~~~~~p--i~~~~~-~~~v~~~~~~ 67 (320)
.+.+++|+|+.|..+++|.|.++-.. +. ..++..++..-. + .++ ++..+. +-.+|+...+
T Consensus 2 ave~~~iINksGglifqref~~~et~lnsneyLiLastlhgV~aI~tq~~p~~--g--ssg~~~l~~~~f~m~I~qT~TG 77 (134)
T COG5122 2 AVEQFFIINKSGGLIFQREFGEGETELNSNEYLILASTLHGVSAILTQTIPLP--G--SSGRLVLYFRNFVMTIFQTTTG 77 (134)
T ss_pred ceeEEEEEecCCcEEEEEeccCCccccCcccEEEEeechhhhhhhhhhcccCC--C--CCceEEEEeccEEEEEEEecCC
Confidence 47899999999999999999754432 11 122222222211 1 122 334443 4567788889
Q ss_pred EEEEEEec-CCCCHHHHHHHHHHHHHHHHHHhcc
Q 020859 68 VYLMTASR-QNCNAASLLFFLHRVVDVFKHYFEE 100 (320)
Q Consensus 68 l~~v~~~~-~~~n~l~~~~~L~~~~~~l~~y~~~ 100 (320)
+-||+++. ...|.++- |+++..+..+|.-+
T Consensus 78 ~kFV~~~~k~t~na~~q---l~kiY~lYsdYV~k 108 (134)
T COG5122 78 TKFVFVAEKRTVNALFQ---LQKIYSLYSDYVTK 108 (134)
T ss_pred cEEEEEecCCchhHHHH---HHHHHHHHHHHhhc
Confidence 99999983 44554443 67777777777643
No 19
>PF04099 Sybindin: Sybindin-like family ; InterPro: IPR007233 Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses. Syndecan-2 induces spine formation by recruiting intracellular vesicles toward postsynaptic sites through the interaction with synbindin []. ; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005801 cis-Golgi network; PDB: 3CUE_C 2J3T_C 2ZMV_B 2JSN_A.
Probab=91.69 E-value=5 Score=33.41 Aligned_cols=94 Identities=10% Similarity=0.189 Sum_probs=54.5
Q ss_pred eeEEEEEcCCCCEEEEEccCCCC----C---hh----------HHHHHHHHhhccCCCC--CCCC--CEEEeCCEEEEE-
Q 020859 5 VSALFLLDIKGRVLVWRDYRGDV----S---AK----------QAERFFTKLIEKDGDA--QSQD--PVVYDNGVSYLF- 62 (320)
Q Consensus 5 I~~i~Il~~~G~~ll~k~y~~~~----~---~~----------~~~~f~~~i~~~~~~~--~~~~--pi~~~~~~~~v~- 62 (320)
|.++||+|+.|..+++|.|.... + .+ .+.+|..++.-.+... .... ..++.+.....+
T Consensus 1 IyslyI~nr~G~lIy~~~~~~~~~~~~~~~~~ne~~ll~g~l~sl~~i~~klsp~~~~~~~~~~~g~~~~~T~~yklh~~ 80 (142)
T PF04099_consen 1 IYSLYIFNRSGGLIYYREWNRSKNEGQPKLSSNEYKLLAGMLHSLKAIASKLSPVDSKPNEPGSSGFESFETDTYKLHCF 80 (142)
T ss_dssp EEEEEEE-TTS-EEEEEETSSSS--E-SSSCHHHHHHHHHHHHHHHHHHHHT-SSSSSS-SSS--SEEEEEESS-EEEEE
T ss_pred CeEEEEEeCCcceeeehhhCCCCccccCCCChhHHHHHHhhHHHHHHHHHHhCCCCcccccccceeEEEEEeCCEEEEEE
Confidence 67899999999999999997643 1 11 2334444444321110 0011 245566766555
Q ss_pred EEeCCEEEEEEecCCCCHHHHHHHHHHHHHHHHHHhc
Q 020859 63 IQHSNVYLMTASRQNCNAASLLFFLHRVVDVFKHYFE 99 (320)
Q Consensus 63 ~~~~~l~~v~~~~~~~n~l~~~~~L~~~~~~l~~y~~ 99 (320)
....++-||++++.+... ..-++++.+.++.-+|.-
T Consensus 81 eT~TGlKFvl~td~~~~~-~~~~l~~~~~~lY~dyV~ 116 (142)
T PF04099_consen 81 ETPTGLKFVLITDPNVPS-LRDELLRIYYELYVDYVV 116 (142)
T ss_dssp E-TTS-EEEEEE-TTCCH-CHHHHHHHHHHHHHHHHH
T ss_pred EcCcCcEEEEEecCCCcc-HHHHHHHHHHHHHHHHHh
Confidence 456799999999988754 345578888888888753
No 20
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=91.53 E-value=6 Score=34.78 Aligned_cols=89 Identities=12% Similarity=0.220 Sum_probs=62.6
Q ss_pred EEEEcCCCCEEEEEccCCCCC-hhHHHHHHHHhhccCCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCHHHHHHH
Q 020859 8 LFLLDIKGRVLVWRDYRGDVS-AKQAERFFTKLIEKDGDAQSQDPVVYDNGVSYLFIQHSNVYLMTASRQNCNAASLLFF 86 (320)
Q Consensus 8 i~Il~~~G~~ll~k~y~~~~~-~~~~~~f~~~i~~~~~~~~~~~pi~~~~~~~~v~~~~~~l~~v~~~~~~~n~l~~~~~ 86 (320)
+|=+=.+|.++++++-.-..+ .+..+.+..++-.. ++..--+.+|++.|-|.+.+++.++|+++.+..--..+.|
T Consensus 4 iYs~VARGTvvLaeft~~~gNf~sva~qiL~klp~~----~n~k~tYs~d~y~Fh~l~~dg~tylcvadds~gR~ipfaF 79 (217)
T KOG0859|consen 4 IYSFVARGTVILAEFTEFSGNFSSIAAQILQKLPSS----SNSKFTYSCDGYTFHYLVEDGLTYLCVADDSAGRQIPFAF 79 (217)
T ss_pred eEEEEecceEEEEeeeeccCCHHHHHHHHHHhCCCC----CCCceEEecCCeEEEEEEeCCeEEEEEEeccccccccHHH
Confidence 344457999999976432222 22334444444322 1123466789999999999999999999988888889999
Q ss_pred HHHHHHHHHHHhcc
Q 020859 87 LHRVVDVFKHYFEE 100 (320)
Q Consensus 87 L~~~~~~l~~y~~~ 100 (320)
|+++.+=+..-+|.
T Consensus 80 Le~Ik~~F~k~YG~ 93 (217)
T KOG0859|consen 80 LERIKEDFKKRYGG 93 (217)
T ss_pred HHHHHHHHHHHhcc
Confidence 99998877666665
No 21
>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=91.51 E-value=3.3 Score=33.55 Aligned_cols=91 Identities=10% Similarity=0.170 Sum_probs=60.7
Q ss_pred eeEEEEEcCCCCEEEEEccCCCCChh-----HHHHHHHHhhccCC--CCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCC
Q 020859 5 VSALFLLDIKGRVLVWRDYRGDVSAK-----QAERFFTKLIEKDG--DAQSQDPVVYDNGVSYLFIQHSNVYLMTASRQN 77 (320)
Q Consensus 5 I~~i~Il~~~G~~ll~k~y~~~~~~~-----~~~~f~~~i~~~~~--~~~~~~pi~~~~~~~~v~~~~~~l~~v~~~~~~ 77 (320)
+.+++|.|++|=+++.-...+ .+.. .+..|-...-+.+. -.+...-+..++++.+++.....+|+..+++.+
T Consensus 17 l~~I~itDrDGvpi~~v~~~~-~~~~~~~~~~~~tf~~a~~Q~~KL~lG~nk~ii~~Y~~~qvv~~~~~pl~it~ias~~ 95 (119)
T PF08923_consen 17 LQAIVITDRDGVPIAKVSSDS-APESAMRPSLLSTFAMAIDQASKLGLGKNKSIIAYYDSYQVVQFNKLPLYITFIASSN 95 (119)
T ss_dssp EEEEEEEETTS-EEEEEE-TT-S-GGGGSHHHHCCHHHHHHHHTTSSS-SEEEEEEEESSEEEEEEEETTEEEEEEEETT
T ss_pred eEEEEEECCCCcEEEEecCCC-CcchhhhhHHHHHHHHHhhcccccCCCCceEEEEEeCCEEEEEEeCCCeEEEEEecCC
Confidence 689999999999988844333 2321 22223322222111 111123466789999999999999999999999
Q ss_pred CCHHHHHHHHHHHHHHHHH
Q 020859 78 CNAASLLFFLHRVVDVFKH 96 (320)
Q Consensus 78 ~n~l~~~~~L~~~~~~l~~ 96 (320)
.|.-.++++-+.+..++++
T Consensus 96 aN~G~il~l~~~L~~~l~~ 114 (119)
T PF08923_consen 96 ANTGLILSLEEELAPILNE 114 (119)
T ss_dssp S-HHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHhHHHHHHHHHH
Confidence 9999999888888888865
No 22
>PF13774 Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3BW6_A 1H8M_A 3EGX_C 2NUP_C 3EGD_C 2NUT_C 3KYQ_A 1IFQ_B 2VX8_D ....
Probab=91.38 E-value=1.5 Score=32.65 Aligned_cols=49 Identities=6% Similarity=0.170 Sum_probs=43.0
Q ss_pred CEEEeCCEEEEEEEeCCEEEEEEecCCCCHHHHHHHHHHHHHHHHHHhc
Q 020859 51 PVVYDNGVSYLFIQHSNVYLMTASRQNCNAASLLFFLHRVVDVFKHYFE 99 (320)
Q Consensus 51 pi~~~~~~~~v~~~~~~l~~v~~~~~~~n~l~~~~~L~~~~~~l~~y~~ 99 (320)
-.++.++..|.+...+++.++|+++.+-+.-.++.||+.+.+-...-++
T Consensus 17 ~s~~~~~~~fh~~~~~~i~~~citd~~~~~r~aF~fL~~i~~~F~~~~~ 65 (83)
T PF13774_consen 17 MSYESGNYVFHYLVEDGIAYLCITDKSYPKRVAFAFLEEIKQEFIQTYG 65 (83)
T ss_dssp EEEEETTEEEEEEEETTEEEEEEEETTS-HHHHHHHHHHHHHHHHHHCT
T ss_pred EEEEECCEEEEEEEcCCeEEEEEEcCCCCcchHHHHHHHHHHHHHHHcC
Confidence 4677888999888899999999999999999999999999988887776
No 23
>PF09201 SRX: SRX; InterPro: IPR015284 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. This entry represents a homologue of the alpha subunit of the SR receptor. Members of this entry consist of a central six-stranded anti-parallel beta-sheet sandwiched by helix alpha1 on one side and helices alpha2-alpha4 on the other. They interact with the small GTPase SR-beta, forming a complex that matches a class of small G protein-effector complexes, including Rap-Raf, Ras-PI3K(gamma), Ras-RalGDS, and Arl2-PDE(delta) []. ; PDB: 1NRJ_A.
Probab=87.70 E-value=12 Score=31.02 Aligned_cols=73 Identities=19% Similarity=0.275 Sum_probs=38.5
Q ss_pred ceeEEEEEcCCCCEEEEEccCC-CCChhHHHHHHHHhhccCCCCC---CCCCEEEe-------CCEEEEEEEe--CCEEE
Q 020859 4 AVSALFLLDIKGRVLVWRDYRG-DVSAKQAERFFTKLIEKDGDAQ---SQDPVVYD-------NGVSYLFIQH--SNVYL 70 (320)
Q Consensus 4 MI~~i~Il~~~G~~ll~k~y~~-~~~~~~~~~f~~~i~~~~~~~~---~~~pi~~~-------~~~~~v~~~~--~~l~~ 70 (320)
|++.+.|++.+|++|++..=-+ ......+.+|..++++.+.... ...-+..+ ++.+++|+.. -.|||
T Consensus 1 MfdQlaIFTpqGqvLyqyN~~gKKFsE~QiN~FIs~lItsP~~~~e~~~~~k~~~i~s~~~~~~~f~~mfh~sKQPeLy~ 80 (148)
T PF09201_consen 1 MFDQLAIFTPQGQVLYQYNCLGKKFSETQINAFISHLITSPVTKKEDSSKSKFLTISSEKKNSRSFSAMFHISKQPELYY 80 (148)
T ss_dssp ---EEEEE-TT-BEEEEEETTS----HHHHHHHHHHHHHS---GGGTT--EEEEE-----------EEEEEEETTTTEEE
T ss_pred CcceeEEeccCceEEEEecccchHHHHHHHHHHHHHHhcCCCcccCCCcceeeEEecccccCCCChheeeeecCCCcEEE
Confidence 8999999999999999944322 2223467889999887653211 11223333 3666666443 47999
Q ss_pred EEEecC
Q 020859 71 MTASRQ 76 (320)
Q Consensus 71 v~~~~~ 76 (320)
|++-.+
T Consensus 81 VvTyae 86 (148)
T PF09201_consen 81 VVTYAE 86 (148)
T ss_dssp EEEESS
T ss_pred EEEecc
Confidence 988654
No 24
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=86.67 E-value=9.8 Score=38.13 Aligned_cols=114 Identities=12% Similarity=0.137 Sum_probs=72.6
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCChhHHHHHHHHhhccCCCCCCCCCEEEeCCEEEEEEEeCC--EEEEEEecCCCCHH
Q 020859 4 AVSALFLLDIKGRVLVWRDYRGDVSAKQAERFFTKLIEKDGDAQSQDPVVYDNGVSYLFIQHSN--VYLMTASRQNCNAA 81 (320)
Q Consensus 4 MI~~i~Il~~~G~~ll~k~y~~~~~~~~~~~f~~~i~~~~~~~~~~~pi~~~~~~~~v~~~~~~--l~~v~~~~~~~n~l 81 (320)
||+.|.|+++.|-+|..+.=.++.-+.-+..|++.++-..... ... +..+.++.=|...|+ +.|+++-..--+-.
T Consensus 1 Mld~faIFtkgG~vLw~~~~~~~~~~~~in~lI~~~ll~er~~-~~~--~~~~~yTlk~q~~N~~~lvfvvvfqki~~L~ 77 (587)
T KOG0781|consen 1 MLDQFAIFTKGGLVLWCYQEVGDNLKGPINALIRSVLLSERGG-VNS--FTFEAYTLKYQLDNQYSLVFVVVFQKILTLT 77 (587)
T ss_pred CcceeeeecCCcEEEEEecccchhccchHHHHHHHHHHHhhcC-ccc--CchhheeEeeeecCCccEEEEEEEeccchhh
Confidence 8999999999998888744333322334566666655432221 112 555566666666664 56666665555666
Q ss_pred HHHHHHHHHHHHHHHHhcccchhHHhhhHH-HHHHHHHHH
Q 020859 82 SLLFFLHRVVDVFKHYFEELEEESLRDNFV-VVYELLDEM 120 (320)
Q Consensus 82 ~~~~~L~~~~~~l~~y~~~l~e~~I~~Nf~-~vy~lLDEi 120 (320)
.+-.+|....+...+-|+..+-..++.|++ +..++|++-
T Consensus 78 yv~~ll~~v~~~f~e~~~~~~~~~l~~n~~~~~~e~lk~r 117 (587)
T KOG0781|consen 78 YVDKLLNDVLNLFREKYDTQSALSLLNNTFDFQEELLKLR 117 (587)
T ss_pred hHHHHHHHHHHHHHHHhccchHHHhhhhhHHHHHHHHHHh
Confidence 677777777777777777777777888864 455666554
No 25
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=79.39 E-value=40 Score=29.15 Aligned_cols=46 Identities=9% Similarity=0.203 Sum_probs=34.3
Q ss_pred EEEeCC-EEEEEEEeCCEEEEEEecCCCCHHHHHHHHHHHHHHHHHHhc
Q 020859 52 VVYDNG-VSYLFIQHSNVYLMTASRQNCNAASLLFFLHRVVDVFKHYFE 99 (320)
Q Consensus 52 i~~~~~-~~~v~~~~~~l~~v~~~~~~~n~l~~~~~L~~~~~~l~~y~~ 99 (320)
+++.+. .-++|+...++-||++++... -.+-.+|+++.++..+|-=
T Consensus 125 ~LetdtF~l~~~QTlTG~KFVvis~~~~--~~aD~lLrKiYelYsDyvl 171 (199)
T KOG3369|consen 125 VLETDTFTLHIFQTLTGTKFVVIAEPGT--QGADSLLRKIYELYSDYVL 171 (199)
T ss_pred EEEeccEEEEEEEccCCcEEEEEecCCc--hhHHHHHHHHHHHHHHHhh
Confidence 444444 457788889999999987655 3566789999999988864
No 26
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=66.56 E-value=73 Score=26.28 Aligned_cols=86 Identities=12% Similarity=0.207 Sum_probs=49.0
Q ss_pred cceeEEEEEcCCCCEEEEEccCCCCC----hh-----------HHHHHHHHhhccCCCCCCCCCEEEeCCEEEEEEEe-C
Q 020859 3 GAVSALFLLDIKGRVLVWRDYRGDVS----AK-----------QAERFFTKLIEKDGDAQSQDPVVYDNGVSYLFIQH-S 66 (320)
Q Consensus 3 ~MI~~i~Il~~~G~~ll~k~y~~~~~----~~-----------~~~~f~~~i~~~~~~~~~~~pi~~~~~~~~v~~~~-~ 66 (320)
|.|.+++|+|++|..|+.+.|..... +. .+..|.+++...+.. +.---+........|... .
T Consensus 1 Mtiy~~yIFdR~g~Cl~y~EW~r~~~s~~~~eee~KL~yGmlFSlkS~v~Kls~~d~k--~~f~sy~Ts~YklhfyeTpt 78 (140)
T KOG3368|consen 1 MTIYNFYIFDRNGVCLFYREWNRTKQSGIPNEEEAKLMYGMLFSLKSFVSKLSPGDVK--DGFLSYKTSKYKLHFYETPT 78 (140)
T ss_pred CeEEEEEEEcCCccEEEehhcccccccCCchhHHHHHHHHHHhhHHHHHHhcCCCCcc--cCeeEEeeceeEEEEEEcCC
Confidence 46889999999999999987753221 11 123344444333211 111122344444444443 5
Q ss_pred CEEEEEEecCCCCHHHHHHHHHHHHH
Q 020859 67 NVYLMTASRQNCNAASLLFFLHRVVD 92 (320)
Q Consensus 67 ~l~~v~~~~~~~n~l~~~~~L~~~~~ 92 (320)
+|.|+..++..... +=+.|+.+..
T Consensus 79 glk~vl~Tdpk~~~--ir~vLq~IYs 102 (140)
T KOG3368|consen 79 GLKFVLNTDPKAGS--IRDVLQYIYS 102 (140)
T ss_pred CcEEEEecCCCccc--HHHHHHHHHH
Confidence 89999998876543 3455666655
No 27
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=60.91 E-value=1.2e+02 Score=27.24 Aligned_cols=49 Identities=10% Similarity=0.232 Sum_probs=43.5
Q ss_pred EEEeCCEEEEEEEeCCEEEEEEecCCCCHHHHHHHHHHHHHHHHHHhcc
Q 020859 52 VVYDNGVSYLFIQHSNVYLMTASRQNCNAASLLFFLHRVVDVFKHYFEE 100 (320)
Q Consensus 52 i~~~~~~~~v~~~~~~l~~v~~~~~~~n~l~~~~~L~~~~~~l~~y~~~ 100 (320)
-++.+.+.|.|+..+++.+.++++.+-+--+++.+|+.+.+-+..-++.
T Consensus 53 Sietg~f~fHfli~~~Vcylvicd~~yP~kLAF~YLedL~~EF~~~~~~ 101 (216)
T KOG0862|consen 53 SIETGPFVFHFLIESGVCYLVICDKSYPRKLAFSYLEDLAQEFDKSYGK 101 (216)
T ss_pred ccccCCeEEEEEecCCEEEEEEecCCCcHHHHHHHHHHHHHHHHHhccc
Confidence 4567789999999999999999999999999999999999888877764
No 28
>PF05228 CHASE4: CHASE4 domain; InterPro: IPR007892 CHASE4 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are upstream of signal transduction pathways in prokaryotes. Specifically, CHASE4 domains are found in histidine kinases in archaea and in predicted diguanylate cyclases/phosphodiesterases in bacteria. Environmental factors that are recognised by CHASE4 domains are not known at this time [].
Probab=28.95 E-value=3.1e+02 Score=22.25 Aligned_cols=20 Identities=40% Similarity=0.748 Sum_probs=16.5
Q ss_pred eeEEEEEcCCCCEEE--EEccC
Q 020859 5 VSALFLLDIKGRVLV--WRDYR 24 (320)
Q Consensus 5 I~~i~Il~~~G~~ll--~k~y~ 24 (320)
+++++++|.+|++++ .+.+.
T Consensus 50 ~d~~~~~d~~g~~~~~~~~~~~ 71 (161)
T PF05228_consen 50 LDLIFILDPDGRVLYSSSKGYD 71 (161)
T ss_pred ccEEEEEcCCCCEEEEeccCcc
Confidence 578999999999999 55544
No 29
>KOG0647 consensus mRNA export protein (contains WD40 repeats) [RNA processing and modification]
Probab=28.52 E-value=1.4e+02 Score=28.22 Aligned_cols=113 Identities=16% Similarity=0.154 Sum_probs=72.7
Q ss_pred EeEeEEEcCCCcEEEEEEEEEEEEEEEeCCCCeEEEEeccchhhhhccCCCCCceeecccCccccccc-cccccCCceEE
Q 020859 179 EHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQGRSTKGKAIDLDDIKFHQCVR-LARFENDRTIS 257 (320)
Q Consensus 179 E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~l~d~~fH~cV~-~~~f~~~~~l~ 257 (320)
-.|.+..+++|. ....|.|++.++.--.|+|.-.+.|.-....+. ....-..+.++.|||--. +..-.++.+.+
T Consensus 202 R~va~f~d~~~~-alGsiEGrv~iq~id~~~~~~nFtFkCHR~~~~----~~~~VYaVNsi~FhP~hgtlvTaGsDGtf~ 276 (347)
T KOG0647|consen 202 RCVACFQDKDGF-ALGSIEGRVAIQYIDDPNPKDNFTFKCHRSTNS----VNDDVYAVNSIAFHPVHGTLVTAGSDGTFS 276 (347)
T ss_pred eEEEEEecCCce-EeeeecceEEEEecCCCCccCceeEEEeccCCC----CCCceEEecceEeecccceEEEecCCceEE
Confidence 356677888888 788999999999999999977777744321000 011223467889999322 23445678888
Q ss_pred EeCCCCceEEEEEEeeCCCCCcEEEEEEEEEcCceEEEEEEEEe
Q 020859 258 FIPPDGSFDLMTYRLNTQVKPLIWVEAQVERHSRSRVEILVKAR 301 (320)
Q Consensus 258 F~PPdg~f~Lm~Y~~~~~~~~P~~v~~~~~~~~~~~~e~~~~l~ 301 (320)
|-..|.+-.|..|.. ..-|+.. +.+... +.-+-|-+...
T Consensus 277 FWDkdar~kLk~s~~---~~qpItc-c~fn~~-G~ifaYA~gYD 315 (347)
T KOG0647|consen 277 FWDKDARTKLKTSET---HPQPITC-CSFNRN-GSIFAYALGYD 315 (347)
T ss_pred EecchhhhhhhccCc---CCCccce-eEecCC-CCEEEEEeecc
Confidence 888888888887753 3345542 555443 33566666554
No 30
>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=27.64 E-value=69 Score=21.07 Aligned_cols=17 Identities=41% Similarity=0.690 Sum_probs=13.3
Q ss_pred EeCCCCceEEEEEEeeC
Q 020859 258 FIPPDGSFDLMTYRLNT 274 (320)
Q Consensus 258 F~PPdg~f~Lm~Y~~~~ 274 (320)
|---||.|+.|.|.-+.
T Consensus 16 fpn~dgtftamtytksk 32 (49)
T PF07151_consen 16 FPNQDGTFTAMTYTKSK 32 (49)
T ss_pred eeCCCCcEEEEEEeecc
Confidence 44559999999998654
No 31
>COG3322 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]
Probab=25.38 E-value=78 Score=29.81 Aligned_cols=36 Identities=11% Similarity=0.323 Sum_probs=26.3
Q ss_pred eeEEEEEcCCCCEEEEEccCCCCChh--HHHHHHHHhh
Q 020859 5 VSALFLLDIKGRVLVWRDYRGDVSAK--QAERFFTKLI 40 (320)
Q Consensus 5 I~~i~Il~~~G~~ll~k~y~~~~~~~--~~~~f~~~i~ 40 (320)
++.+|++|.+|++++++.+....-.+ ..+.+.+.+.
T Consensus 104 ~d~vf~vd~~G~~vy~~~~d~~t~~~~~~~~~L~~~i~ 141 (295)
T COG3322 104 LDGVFVVDPSGKLVYSKLVDQETATELPLPESLLEDIR 141 (295)
T ss_pred ccEEEEECCCCCEEEEeeeccccccccCCcHHHHHHHh
Confidence 47899999999999999996544332 2356666655
No 32
>PF00235 Profilin: Profilin; InterPro: IPR002097 Profilin is a small eukaryotic protein that binds to monomeric actin (G-actin) in a 1:1 ratio thus preventing the polymerisation of actin into filaments (F-actin). It can also in certain circumstance promote actin polymerisation. Profilin also binds to polyphosphoinositides such as PIP2. Overall sequence similarity among profilin from organisms which belong to different phyla (ranging from fungi to mammals) is low, but the N-terminal region is relatively well conserved. That region is thought to be involved in the binding to actin. A protein structurally similar to profilin is present in the genome of Variola virus and Vaccinia virus (gene A42R). Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Ara t 8, Bet v 2, Cyn d 12, Hel a 2, Mer a 1 and Phl p 11.; GO: 0003779 actin binding, 0007010 cytoskeleton organization, 0015629 actin cytoskeleton; PDB: 1ACF_A 3NEC_C 2V8F_B 2V8C_A 2VK3_A 2JKF_A 2JKG_A 1F2K_B 2ACG_A 1YPR_B ....
Probab=25.33 E-value=3.3e+02 Score=21.25 Aligned_cols=87 Identities=7% Similarity=0.103 Sum_probs=49.1
Q ss_pred eeEEEEEcCCCCEEEEEccCCCCChhHHHHHHHHhhccCCCCCCCCCEEEeCCE-------------------EEEEEEe
Q 020859 5 VSALFLLDIKGRVLVWRDYRGDVSAKQAERFFTKLIEKDGDAQSQDPVVYDNGV-------------------SYLFIQH 65 (320)
Q Consensus 5 I~~i~Il~~~G~~ll~k~y~~~~~~~~~~~f~~~i~~~~~~~~~~~pi~~~~~~-------------------~~v~~~~ 65 (320)
+.+..|++.+|.+..+.---...+...+..+...+...... ...=+.++|. -++..+.
T Consensus 16 ~~~aaI~~~dG~vwA~s~~f~~~~~~E~~~i~~~f~~~~~~---~~~gi~l~G~kY~~~~~d~~~i~~k~~~~G~~i~kt 92 (121)
T PF00235_consen 16 ITKAAIIGSDGSVWASSPGFSNISPEEAKAIIKAFNNPSKF---PSNGITLGGKKYIVLRADDNSIYGKKGKGGIIIVKT 92 (121)
T ss_dssp ESEEEEEETTSSEEEEETTGGGCSHHHHHHHHHHHHSSSHH---HHH-EEETTEEEEEEEEETTEEEEEETTEEEEEEEC
T ss_pred EeEEEEEcCCCCEEEecCCCCCCCHHHHHHHHHHhcCchhc---ccCCeEEcCcEeEEEecCCceEEeeCCCCcEEEEEC
Confidence 67778888999887764421012233333333333222100 0111233333 3444445
Q ss_pred CCEEEEEEecCCCCHHHHHHHHHHHHHHH
Q 020859 66 SNVYLMTASRQNCNAASLLFFLHRVVDVF 94 (320)
Q Consensus 66 ~~l~~v~~~~~~~n~l~~~~~L~~~~~~l 94 (320)
+..++++..+.+.+|-.+.....++++.|
T Consensus 93 ~~~ivIg~y~~~~~~~~~~~~v~~lA~yL 121 (121)
T PF00235_consen 93 KQAIVIGMYDESIQPGNCNKAVEKLADYL 121 (121)
T ss_dssp SSEEEEEEEETTSTHHHHHHHHHHHHHHH
T ss_pred CCEEEEEEeCCCCCHHHHHHHHHHHHhhC
Confidence 56788888888889988888888888765
No 33
>KOG1766 consensus Enhancer of rudimentary [General function prediction only]
Probab=25.14 E-value=1e+02 Score=23.89 Aligned_cols=42 Identities=7% Similarity=0.337 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHHHHhcc--cchhHHhhhHHHHHHHHHHHhcCC
Q 020859 83 LLFFLHRVVDVFKHYFEE--LEEESLRDNFVVVYELLDEMMDFG 124 (320)
Q Consensus 83 ~~~~L~~~~~~l~~y~~~--l~e~~I~~Nf~~vy~lLDEiid~G 124 (320)
+-+.+..+.++.++++++ .+...|-.....+|+.+|.+.|-.
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 557788889999999987 366778888999999999998764
Done!