Query 021735
Match_columns 308
No_of_seqs 152 out of 1179
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 05:16:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021735.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021735hhsearch_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 7.7E-77 1.7E-81 534.5 27.6 301 4-307 1-327 (446)
2 KOG0937 Adaptor complexes medi 100.0 4.8E-66 1E-70 482.9 28.9 302 5-307 1-303 (424)
3 KOG2740 Clathrin-associated pr 100.0 3.2E-61 7E-66 437.1 23.3 286 4-304 1-301 (418)
4 PF00928 Adap_comp_sub: Adapto 100.0 1.4E-35 3E-40 270.5 17.5 142 159-307 1-142 (262)
5 PF01217 Clat_adaptor_s: Clath 100.0 3.4E-29 7.5E-34 208.2 17.6 135 4-141 1-138 (141)
6 KOG2635 Medium subunit of clat 100.0 1.8E-27 3.8E-32 221.7 24.8 271 3-292 1-391 (512)
7 COG5030 APS2 Clathrin adaptor 99.9 5.2E-23 1.1E-27 164.4 13.8 132 4-138 1-135 (152)
8 KOG0934 Clathrin adaptor compl 99.9 8.4E-22 1.8E-26 157.3 7.4 129 4-135 1-132 (145)
9 KOG0936 Clathrin adaptor compl 99.8 3.6E-20 7.7E-25 150.1 13.5 157 4-163 1-166 (182)
10 KOG0935 Clathrin adaptor compl 99.8 2E-19 4.4E-24 140.3 11.8 134 4-139 1-137 (143)
11 KOG2677 Stoned B synaptic vesi 99.8 8.8E-21 1.9E-25 183.4 3.6 132 166-298 582-722 (922)
12 KOG3343 Vesicle coat complex C 99.8 4.2E-18 9.2E-23 139.3 13.5 139 4-144 8-149 (175)
13 COG5541 RET3 Vesicle coat comp 99.3 6.9E-12 1.5E-16 102.6 9.1 139 4-144 7-156 (187)
14 PF03164 Mon1: Trafficking pro 96.6 0.025 5.3E-07 55.3 11.4 90 6-99 12-104 (415)
15 PF15001 AP-5_subunit_s1: AP-5 95.0 0.26 5.6E-06 42.7 9.8 80 57-136 103-183 (189)
16 PF08923 MAPKK1_Int: Mitogen-a 94.2 0.76 1.7E-05 37.0 10.2 92 5-96 17-114 (119)
17 KOG0997 Uncharacterized conser 93.8 0.58 1.3E-05 45.9 10.3 75 6-84 118-195 (523)
18 COG5122 TRS23 Transport protei 93.7 1.6 3.4E-05 34.6 10.7 89 4-99 2-107 (134)
19 PF10291 muHD: Muniscin C-term 93.0 6 0.00013 36.1 15.3 115 173-303 3-131 (257)
20 PF04099 Sybindin: Sybindin-li 92.8 4.2 9.2E-05 33.6 12.9 93 5-98 1-115 (142)
21 PF13774 Longin: Regulated-SNA 92.6 0.94 2E-05 33.5 7.9 49 51-99 17-65 (83)
22 KOG0859 Synaptobrevin/VAMP-lik 92.0 2.7 5.8E-05 36.7 10.7 89 8-100 4-93 (217)
23 PF09201 SRX: SRX; InterPro: 88.7 7.8 0.00017 31.9 10.2 73 4-76 1-86 (148)
24 KOG0781 Signal recognition par 87.6 8.5 0.00018 38.3 11.5 114 4-120 1-117 (587)
25 KOG3369 Transport protein part 82.7 19 0.00042 30.8 10.0 46 52-99 125-171 (199)
26 KOG0862 Synaptobrevin/VAMP-lik 66.1 85 0.0018 27.9 10.1 49 52-100 53-101 (216)
27 KOG3368 Transport protein part 59.8 96 0.0021 25.4 10.5 90 3-98 1-109 (140)
28 KOG0647 mRNA export protein (c 30.2 1.5E+02 0.0032 28.0 6.0 89 179-272 202-291 (347)
29 PF00235 Profilin: Profilin; 27.6 2.9E+02 0.0064 21.4 9.1 87 5-94 16-121 (121)
30 PF05228 CHASE4: CHASE4 domain 23.4 3.9E+02 0.0085 21.4 7.5 21 5-25 50-72 (161)
31 COG3322 Predicted periplasmic 23.3 90 0.0019 29.2 3.4 36 5-40 104-141 (295)
32 PF07151 DUF1391: Protein of u 21.8 1.1E+02 0.0023 20.0 2.5 18 257-274 15-32 (49)
33 PF08784 RPA_C: Replication pr 21.6 1.3E+02 0.0027 22.9 3.5 23 108-130 77-99 (102)
34 KOG0283 WD40 repeat-containing 20.3 1.3E+02 0.0028 31.6 4.1 36 179-216 410-446 (712)
35 PF01535 PPR: PPR repeat; Int 20.3 92 0.002 17.2 1.9 18 108-125 14-31 (31)
No 1
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=7.7e-77 Score=534.50 Aligned_cols=301 Identities=40% Similarity=0.729 Sum_probs=276.9
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCChhHHHHHHHHhccccCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCHHHH
Q 021735 4 AASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAASI 83 (308)
Q Consensus 4 MI~~i~Il~~~G~~ll~r~y~~~~~~~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~Ly~v~v~~~~~n~l~~ 83 (308)
||+++||+|.+|++++.|.||+|..++..+.|+-++.++.. ..+|+..++++.|+|.+.++||+++++.+|.|.+.+
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 MISGLFIYNLRGEVLINKTFRDDLKRSIVDIFRVQVINNLD---VRSPVLTIGSTTFHHIRSSNLWLVAITKSNANVAAV 77 (446)
T ss_pred CcceEEEEeccCcEEEehhhhhhhhhhHHHHHHHhhhhccc---cCCCeeEecceeEEEEeeccEEEEEEecCCCchhhH
Confidence 89999999999999999999999999999999999998743 358999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcchhHHHHhhhHHHHHHHHHHHHcCCeeeecChHHHHHHhcccccccccc----C-----CCC--
Q 021735 84 LLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYRMEVT----Q-----RPP-- 152 (308)
Q Consensus 84 ~~~L~~~~~~l~~y~~~l~e~~I~~n~~~v~~lLDEiid~G~p~~t~~~~L~~~i~~~~~~~~~~----~-----~~~-- 152 (308)
++||..+..++..|||+.+|+.|++||.++||+||||+|+||||+|++++|+.+|..+++..+-. . .++
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 99999999999999999999999999999999999999999999999999999999988765411 1 111
Q ss_pred --CcccCCCcCcccCCccccceEEEEEEEeEeEEEccCCcEEEEEEEEEEEEEEEeCCCCeEEEeeccchhhhh-cc---
Q 021735 153 --MAVTNAVSWRSEGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEA-QG--- 226 (308)
Q Consensus 153 --~~~~~~~~wR~~~~~~~~nei~vdv~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~-~~--- 226 (308)
++.++.++||++|++|+|||+|+||+|+++.+++++|++++++|+|.|.|+++|||||+|++||||.+.+.. ++
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 334567999999999999999999999999999999999999999999999999999999999999987762 21
Q ss_pred --------CC-CCCceeecccccccccccccCccCCCeEEEeCCCCceEEEEEEecCCCCCcEEEEEEEEEcCceEEEEE
Q 021735 227 --------RS-TKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSRIEIM 297 (308)
Q Consensus 227 --------~~-~~~~~~~l~~~~fH~cV~~~~f~~~~~i~F~PPdg~f~Lm~Y~~~~~~~~P~~v~~~~~~~~~~~~~~~ 297 (308)
++ +....+.|+||+||+||++++|++++.|+|+||||+|+||+||++.+.++||+|.|.+++.+.+++++.
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 11 133458899999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeeccCCC
Q 021735 298 VKARSQFKER 307 (308)
Q Consensus 298 i~l~~~~~~~ 307 (308)
+++|++||++
T Consensus 318 i~iks~f~~k 327 (446)
T KOG0938|consen 318 ITIKSLFPPK 327 (446)
T ss_pred EEEeccCCch
Confidence 9999999875
No 2
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=4.8e-66 Score=482.90 Aligned_cols=302 Identities=62% Similarity=1.038 Sum_probs=278.0
Q ss_pred eeEEEEEcCCCCEEEEEccCCCCChhHHHHHHHHhccccCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCHHHHH
Q 021735 5 ASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAASIL 84 (308)
Q Consensus 5 I~~i~Il~~~G~~ll~r~y~~~~~~~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~Ly~v~v~~~~~n~l~~~ 84 (308)
++|+||+|.+|++|++|.||++.+.+..+.|++++.... .....+|++..+|+.|+|.+++++|++++++.|.+++.++
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 589999999999999999999998899999998666532 2234679999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhcchhHHHHhhhHHHHHHHHHHHHcCCeeeecChHHHHHHhccccccccccC-CCCCcccCCCcCcc
Q 021735 85 LFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYRMEVTQ-RPPMAVTNAVSWRS 163 (308)
Q Consensus 85 ~~L~~~~~~l~~y~~~l~e~~I~~n~~~v~~lLDEiid~G~p~~t~~~~L~~~i~~~~~~~~~~~-~~~~~~~~~~~wR~ 163 (308)
+||+++++++.+||+.+.|+.++.||.++||+|||++||||||.|++..|++++..++...+... ++|.+.++.++||+
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 99999999999999999999999999999999999999999999999999999999966543322 45778888899999
Q ss_pred cCCccccceEEEEEEEeEeEEEccCCcEEEEEEEEEEEEEEEeCCCCeEEEeeccchhhhhccCCCCCceeecccccccc
Q 021735 164 EGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRSTKGKAIDLDDIKFHQ 243 (308)
Q Consensus 164 ~~~~~~~nei~vdv~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~l~~~~fH~ 243 (308)
.|++|+|||+|+||+|+++++++++|.+++++|.|+|+|||+|+|||+++|+||+....+..+..+++..+.++|++||+
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 99999999999999999999999999999999999999999999999999999999888777766666789999999999
Q ss_pred cccccCccCCCeEEEeCCCCceEEEEEEecCCCCCcEEEEEEEEEcCceEEEEEEEEeeccCCC
Q 021735 244 CVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSRIEIMVKARSQFKER 307 (308)
Q Consensus 244 cV~~~~f~~~~~i~F~PPdg~f~Lm~Y~~~~~~~~P~~v~~~~~~~~~~~~~~~i~l~~~~~~~ 307 (308)
||++++|+.+|.|+|+||||+|+||+||++....|++.+....+.++..|+++.+++++.|+++
T Consensus 240 ~v~l~~fd~dr~i~FiPPdGeF~Lm~Y~ls~~vkPli~~~~~~~~~~~~ri~i~~K~~~~fk~~ 303 (424)
T KOG0937|consen 240 CVRLSRFDNDRTISFIPPDGEFELMRYRLSTHVKPLIWFYQLIEEHSRSRIEVMVKLREQFKSR 303 (424)
T ss_pred eechhhccCCceEEecCCCCceEEEEEEecCCCCCeEEeeeeeeeccceeEEEEEechhhcCCc
Confidence 9999999999999999999999999999999888888876666667899999999999999975
No 3
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=3.2e-61 Score=437.06 Aligned_cols=286 Identities=34% Similarity=0.631 Sum_probs=254.7
Q ss_pred ceeEEEEEcCCCCEEEEEccCC-CCChhHHHHHHHHhccccCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCHHH
Q 021735 4 AASALFLLDIKGRVLIWRDYRG-DVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAAS 82 (308)
Q Consensus 4 MI~~i~Il~~~G~~ll~r~y~~-~~~~~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~Ly~v~v~~~~~n~l~ 82 (308)
||.++|+.|.+|++++++.+++ ...|+.++.|+........ ....+|++....++++..-++++||++++..+..|++
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 MILSIFLIDTSGDLLLEKHLKGSTVVRSICDYFFEDQSSDDD-LEHVPPVISTPHHYLFSVYRDLIFFCAVSTVETPPLM 79 (418)
T ss_pred CeeEEEEEcCCchhhhhHhhCCceeeeehHHHHHHhhhhccc-cccCCceecCCceeeeeeeccCcEEEEEEeccCCChh
Confidence 8999999999999999999994 4557788888887765432 2245678888888888888999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcchhHHHHhhhHHHHHHHHHHHHcCCeeeecChHHHHHHhcccccccccc----------CCCC
Q 021735 83 ILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYRMEVT----------QRPP 152 (308)
Q Consensus 83 ~~~~L~~~~~~l~~y~~~l~e~~I~~n~~~v~~lLDEiid~G~p~~t~~~~L~~~i~~~~~~~~~~----------~~~~ 152 (308)
+++||+++++++.+|||+++|.+|++|++.||++||||+|+|+|..||+|.||++|..++.+.+.. ...|
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 999999999999999999999999999999999999999999999999999999999999887432 1456
Q ss_pred CcccCCCcCcccCCccccceEEEEEEEeEeEEEccCCcEEEEEEEEEEEEEEEeCCCCeEEEeeccchhhhhccCCCCCc
Q 021735 153 MAVTNAVSWRSEGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRSTKGK 232 (308)
Q Consensus 153 ~~~~~~~~wR~~~~~~~~nei~vdv~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~ 232 (308)
+++.+.+|||+.+.+|.+||.||||+|+++|+++++|..+.++|.|.|.|+|+|+|||++.|.|+++.
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 77777899999999999999999999999999999999999999999999999999999999998862
Q ss_pred eeecccccccccccccCccCCCeEEEeCCCCceEEEEEEecCC--CCCcEEEEEEEEEcCc--eEEEEEEEEeecc
Q 021735 233 AIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQ--VKPLIWVEAQIERHSR--SRIEIMVKARSQF 304 (308)
Q Consensus 233 ~~~l~~~~fH~cV~~~~f~~~~~i~F~PPdg~f~Lm~Y~~~~~--~~~P~~v~~~~~~~~~--~~~~~~i~l~~~~ 304 (308)
.|+|++|||||+.++|+++++|+|+||||+|+||+||++.. ...|..++++++-.+. .|++++++-+...
T Consensus 228 --~L~dvsfHpcVr~krwe~~~~lsFIPPDGkFrLlsy~v~~~~~v~~pvyv~~~i~l~~~~~~ri~~tvg~~~~~ 301 (418)
T KOG2740|consen 228 --LLGDVSFHPCVRYKRWESHSVLSFIPPDGKFRLLSYRVDAQNQVAIPVYVKNSISLDSNHQGRISLTVGPKKKM 301 (418)
T ss_pred --ccCCcccccceeecccccccceEEcCCCCcEEEEEEEEehhhccccceEEeeeeccCCCceEEEEEeccccccc
Confidence 58999999999999999999999999999999999999754 4889999999987544 4666666555443
No 4
>PF00928 Adap_comp_sub: Adaptor complexes medium subunit family; InterPro: IPR008968 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. This entry represents the C-terminal domain of the mu subunit from various clathrin adaptors (AP1, AP2 and AP3) []. The C-teminal domain has an immunoglobulin-like beta-sandwich fold consisting of 9 strands in 2 sheets with a Greek key topology, similar to that found in cytochrome f and certain transcription factors []. The mu subunit regulates the coupling of clathrin lattices with particular membrane proteins by self-phosphorylation via a mechanism that is still unclear []. The mu subunit possesses a highly conserved N-terminal domain of around 230 amino acids, which may be the region of interaction with other AP proteins; a linker region of between 10 and 42 amino acids; and a less well-conserved C-terminal domain of around 190 amino acids, which may be the site of specific interaction with the protein being transported in the vesicle []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 1H6E_A 3L81_A 1W63_V 4EMZ_A 4EN2_A 2VGL_M 3ML6_F 2PR9_A 2JKT_M 1I31_A ....
Probab=100.00 E-value=1.4e-35 Score=270.47 Aligned_cols=142 Identities=43% Similarity=0.853 Sum_probs=120.9
Q ss_pred CcCcccCCccccceEEEEEEEeEeEEEccCCcEEEEEEEEEEEEEEEeCCCCeEEEeeccchhhhhccCCCCCceeeccc
Q 021735 159 VSWRSEGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRSTKGKAIDLDD 238 (308)
Q Consensus 159 ~~wR~~~~~~~~nei~vdv~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~l~~ 238 (308)
+|||+.+.+|++|||||||+|+++|+++++|.++.++|.|+|.|+++|+|+|+|+|+||++... ..+++.++|
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 5899999999999999999999999999999999999999999999999999999999998433 235678999
Q ss_pred ccccccccccCccCCCeEEEeCCCCceEEEEEEecCCCCCcEEEEEEEEEcCceEEEEEEEEeeccCCC
Q 021735 239 IKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLSTQVKPLIWVEAQIERHSRSRIEIMVKARSQFKER 307 (308)
Q Consensus 239 ~~fH~cV~~~~f~~~~~i~F~PPdg~f~Lm~Y~~~~~~~~P~~v~~~~~~~~~~~~~~~i~l~~~~~~~ 307 (308)
++||+||++++|+++|.|+|+||||+|+||+||++....+||.++|++.+.+++++++.++++++++++
T Consensus 74 ~~fH~cV~~~~~~~~~~i~f~PPdg~f~Ll~Yr~~~~~~~P~~i~~~~~~~~~~~~~v~i~~~~~~~~~ 142 (262)
T PF00928_consen 74 VSFHPCVDLSKFESDRVISFIPPDGEFTLLRYRVSSNSPLPFKITCWVSEKSSGRFEVTIELESNFPNK 142 (262)
T ss_dssp EEEETTEECCCCCSHTEEEE---SEEEEEEEEEEESSS--SEEEEEEEEEETTTEEEEEEEEEE-S-TT
T ss_pred eeeccccCccccccccceecCCCCceEEEEEEEccCCCCCCcEEEEEeccCCCceEEEEEEecccCCCC
Confidence 999999999999999999999999999999999998899999999999998889999999999998763
No 5
>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=99.97 E-value=3.4e-29 Score=208.20 Aligned_cols=135 Identities=24% Similarity=0.471 Sum_probs=115.8
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCChh---HHHHHHHHhccccCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCH
Q 021735 4 AASALFLLDIKGRVLIWRDYRGDVSAI---QAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNA 80 (308)
Q Consensus 4 MI~~i~Il~~~G~~ll~r~y~~~~~~~---~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~Ly~v~v~~~~~n~ 80 (308)
||+|++|+|++|+++++|||++..... ..+++.+....++ +..+|++.+++++++|++.++|||+++++.++||
T Consensus 1 MI~~i~i~n~~G~~i~~k~y~~~~~~~~~~~~~~~~~~~~~~~---~~~~~i~~~~~~~~vy~~~~dl~~~~v~~~~eNe 77 (141)
T PF01217_consen 1 MIKAILILNSQGKRILSKYYRDVSEEERQKLFEKFIKKKSSRN---SKQSPIFEHDNYRIVYKRYSDLYFVVVGDENENE 77 (141)
T ss_dssp SEEEEEEEETTSEEEEEEESSTSTSHHHHHHHHHHHHHHHTSS---SSSTSEEEETTEEEEEEEETTEEEEEEESSTSBH
T ss_pred CEEEEEEEcCCCCEEEehhcCCccHHHHHHHHHHHHHHHHhcc---cccceeeecccceeeeEeeccEEEEEEeecccch
Confidence 999999999999999999997654432 2233333333332 2358999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhcchhHHHHhhhHHHHHHHHHHHHcCCeeeecChHHHHHHhccc
Q 021735 81 ASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTD 141 (308)
Q Consensus 81 l~~~~~L~~~~~~l~~y~~~l~e~~I~~n~~~v~~lLDEiid~G~p~~t~~~~L~~~i~~~ 141 (308)
++++++|++++++|+.||++++|.+|++||+.+|++||||+|+|+|++||++.|.+.+.+.
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 9999999999999999999999999999999999999999999999999999999998764
No 6
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.96 E-value=1.8e-27 Score=221.70 Aligned_cols=271 Identities=17% Similarity=0.281 Sum_probs=224.9
Q ss_pred cceeEEEEEcCCCCEEEEEccCCCCChhH----HHHHHHHhccccCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCC
Q 021735 3 GAASALFLLDIKGRVLIWRDYRGDVSAIQ----AERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNC 78 (308)
Q Consensus 3 ~MI~~i~Il~~~G~~ll~r~y~~~~~~~~----~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~Ly~v~v~~~~~ 78 (308)
+|+-++-|++..|+.+++|+|+ ++++.. +.+|.+.+... .++.+++.+.++|||+..+++|+|.+|..+.
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 5678899999999999999999 567654 44666666532 4689999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHHHHHhcchhHHHHhhhHHHHHHHHHHHHcCCeeeecChHHHHHHhccccccccccC---------
Q 021735 79 NAASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYRMEVTQ--------- 149 (308)
Q Consensus 79 n~l~~~~~L~~~~~~l~~y~~~l~e~~I~~n~~~v~~lLDEiid~G~p~~t~~~~L~~~i~~~~~~~~~~~--------- 149 (308)
|.+..++.|+.|.+++.+||..+.|..|.+|...+...+||++..||-...+..+++.|..++++++|++.
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 99999999999999999999999999999999999999999999999999999999999999999887420
Q ss_pred ------------------------------------------------------CCC---Ccc-cCCCcCc---------
Q 021735 150 ------------------------------------------------------RPP---MAV-TNAVSWR--------- 162 (308)
Q Consensus 150 ------------------------------------------------------~~~---~~~-~~~~~wR--------- 162 (308)
..| .++ ....|-+
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 000 000 0000000
Q ss_pred --------------------------------ccCCccccceEEEEEEEeEeEEEccCCcEEEEEEEEEEEEEEEeCCCC
Q 021735 163 --------------------------------SEGIRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMP 210 (308)
Q Consensus 163 --------------------------------~~~~~~~~nei~vdv~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P 210 (308)
+....-.++-+++.+.|+|++.++++|.+...+++|.+.++.--.-..
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 000111234499999999999999999999999999999999988888
Q ss_pred eEEEeeccchhhhhccCCCCCceeecccccccccccccCccCCCeEEEeCCCCce------EEEEEEecC--CCCCcEEE
Q 021735 211 ECKLGLNDRVLLEAQGRSTKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSF------DLMTYRLST--QVKPLIWV 282 (308)
Q Consensus 211 ~~~l~ln~~~~~~~~~~~~~~~~~~l~~~~fH~cV~~~~f~~~~~i~F~PPdg~f------~Lm~Y~~~~--~~~~P~~v 282 (308)
.+.|.|++... . =-++++||.+|++.|.++..|...+|+..| -|++||... ....|+++
T Consensus 315 ~i~lkl~n~~~----------~---g~q~ktHPNlDK~~f~s~s~iglk~~~K~FPvn~~VGvLkWR~~~~des~iPlTi 381 (512)
T KOG2635|consen 315 DIELKLANGRD----------K---GTQLKTHPNLDKKVFLSSSLIGLKRPEKPFPVNSDVGVLKWRMVDEDESEIPLTI 381 (512)
T ss_pred ceEEEEcCCCC----------c---ceeeeeCCCcchhhhccccccccccCCCCCCcCCcceEEEEeecccccccCceEE
Confidence 99999977421 1 247899999999999999999999999988 799999876 45899999
Q ss_pred EEEEEEcCce
Q 021735 283 EAQIERHSRS 292 (308)
Q Consensus 283 ~~~~~~~~~~ 292 (308)
+||.++.+++
T Consensus 382 ncWPSes~~g 391 (512)
T KOG2635|consen 382 NCWPSESGNG 391 (512)
T ss_pred EeccccCCCC
Confidence 9999887654
No 7
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=99.90 E-value=5.2e-23 Score=164.41 Aligned_cols=132 Identities=14% Similarity=0.236 Sum_probs=118.1
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCCh---hHHHHHHHHhccccCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCH
Q 021735 4 AASALFLLDIKGRVLIWRDYRGDVSA---IQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNA 80 (308)
Q Consensus 4 MI~~i~Il~~~G~~ll~r~y~~~~~~---~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~Ly~v~v~~~~~n~ 80 (308)
||++++|+|++|++++.|||.+.... ..+...+..+.+++ ++++.+++.++..++|+++++|||+++.+.++|+
T Consensus 1 ~i~~vli~nrqgk~RL~K~yt~~~~~e~~kli~~i~~lIs~R~---~ke~N~~e~k~~kiVYrrYA~LyF~f~Vd~~dnE 77 (152)
T COG5030 1 MIKFVLIFNRQGKPRLVKWYTPVSDPEQAKLIADIYELISARK---PKESNFIEGKNEKIVYRRYATLYFVFGVDNDDNE 77 (152)
T ss_pred CeEEEEEEcCCCceeeeEeeccCCcHHHHHHHHHHHHHHHcCC---chhcccccccCcEEEeeecCcEEEEEEEcCCCCc
Confidence 89999999999999999999764331 25566777777764 2467899999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhcchhHHHHhhhHHHHHHHHHHHHcCCeeeecChHHHHHHh
Q 021735 81 ASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFI 138 (308)
Q Consensus 81 l~~~~~L~~~~~~l~~y~~~l~e~~I~~n~~~v~~lLDEiid~G~p~~t~~~~L~~~i 138 (308)
+.+++++|.|+++|+.|||++||.++..||..+|.+||||+-+|..++++++.+.+.+
T Consensus 78 l~iL~lIh~FVE~lDr~FgnVCELdlIFNF~kv~~ILdE~i~gG~i~Es~~~~vl~~v 135 (152)
T COG5030 78 LIILELIHNFVEILDRFFGNVCELDLIFNFQKVYAILDEMILGGEIIESSKNEVLEHV 135 (152)
T ss_pred chHHHHHHHHHHHHHHHhccceeeEeEeeHHHHHHHHHHHHhCCeeeecCHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999998766544
No 8
>KOG0934 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.86 E-value=8.4e-22 Score=157.31 Aligned_cols=129 Identities=16% Similarity=0.221 Sum_probs=113.4
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCCh--h-HHHHHHHHhccccCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCH
Q 021735 4 AASALFLLDIKGRVLIWRDYRGDVSA--I-QAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNA 80 (308)
Q Consensus 4 MI~~i~Il~~~G~~ll~r~y~~~~~~--~-~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~Ly~v~v~~~~~n~ 80 (308)
||.++++.+++|+++++|||...... . ......+.+.+++ +..|.++++++...||+++++|||++....++|+
T Consensus 1 mi~f~LlvsrQGk~rL~k~y~~~~~~er~~i~re~i~~~Lar~---pk~csfie~kd~kvVyrryasl~f~~~v~~~dNE 77 (145)
T KOG0934|consen 1 MIKFFLLVSRQGKTRLQKWYEALSIKERKKIERELIKSVLARK---PKMCSFIEYKDEKVVYRRYASLFFCVGVEDNDNE 77 (145)
T ss_pred CeEEEEEEeccCceehhHHHhhhcHHHHHHHHHHHHHHHHhCC---cccccchhccCceehhhhhhhEEEEEEEecCCch
Confidence 89999999999999999999874432 2 3334555555544 3578999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhcchhHHHHhhhHHHHHHHHHHHHcCCeeeecChHHHH
Q 021735 81 ASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILS 135 (308)
Q Consensus 81 l~~~~~L~~~~~~l~~y~~~l~e~~I~~n~~~v~~lLDEiid~G~p~~t~~~~L~ 135 (308)
+.++|++|+++++|+.|||++||.+|..||..+|.+|||++-+|..|++..+...
T Consensus 78 L~~LE~IH~~vE~lDkYFg~VCELDiiFNfekay~ILde~~~~g~~~e~~k~~~~ 132 (145)
T KOG0934|consen 78 LAILEFIHNYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEIQETSKNDVL 132 (145)
T ss_pred hhHHHHHHHHHHHHHHHhccceeeEEEEehHhHHHHHHHHhcCcchHhhhcccHH
Confidence 9999999999999999999999999999999999999999999999999887533
No 9
>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.84 E-value=3.6e-20 Score=150.14 Aligned_cols=157 Identities=15% Similarity=0.111 Sum_probs=126.5
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCC---hhHHHHHHHHhccccCCCCCCCCEEEe------CCEEEEEEEeCCEEEEEEe
Q 021735 4 AASALFLLDIKGRVLIWRDYRGDVS---AIQAERFFTKFIEKEGDPQSQNPVVFD------NGVTYMFIQHNNVYLMAAS 74 (308)
Q Consensus 4 MI~~i~Il~~~G~~ll~r~y~~~~~---~~~~~~f~~~i~~~~~~~~~~~pii~~------~~~~~v~~~~~~Ly~v~v~ 74 (308)
||+|++|+|.+|++++.|+|..-.. +..+...+..+.++++ ..+.+++. .+.+.+|+.+..|||+.+.
T Consensus 1 MI~AvlifNn~gkPRL~KFY~p~~~~~Qq~lir~vf~lvs~R~~---n~~nFLe~~~l~g~~d~rlIYrhYATLYFvfvv 77 (182)
T KOG0936|consen 1 MIKAVLIFNNKGKPRLVKFYTPVDEEKQQQLIREVFHLVSKRPD---NVCNFLEGNSLIGGSDNRLIYRHYATLYFVFVV 77 (182)
T ss_pred CeeEEEEecCCCCcceeeecCcCChHHHHHHHHHHHHHHHcCCc---hHhhhhccccccCCccceeehheeeeEEEEEEE
Confidence 9999999999999999999987432 2355566667776653 24555543 3689999999999999999
Q ss_pred cCCCCHHHHHHHHHHHHHHHHHHhcchhHHHHhhhHHHHHHHHHHHHcCCeeeecChHHHHHHhccccccccccCCCCCc
Q 021735 75 RQNCNAASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYRMEVTQRPPMA 154 (308)
Q Consensus 75 ~~~~n~l~~~~~L~~~~~~l~~y~~~l~e~~I~~n~~~v~~lLDEiid~G~p~~t~~~~L~~~i~~~~~~~~~~~~~~~~ 154 (308)
++.++++.++++++.|++.|+..|.++||.++..|++.++.+|+|++.+|...+|+.+.+...+....-.++.....+.+
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 99999999999999999999999999999999999999999999999999999999999888887654444322223333
Q ss_pred ccCCCcCcc
Q 021735 155 VTNAVSWRS 163 (308)
Q Consensus 155 ~~~~~~wR~ 163 (308)
.++...|+.
T Consensus 158 p~~~~~~~~ 166 (182)
T KOG0936|consen 158 PTRAVFAVK 166 (182)
T ss_pred chhhhhhhh
Confidence 333444553
No 10
>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.81 E-value=2e-19 Score=140.25 Aligned_cols=134 Identities=18% Similarity=0.169 Sum_probs=111.4
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCC--h-hHHHHHHHHhccccCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCH
Q 021735 4 AASALFLLDIKGRVLIWRDYRGDVS--A-IQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNA 80 (308)
Q Consensus 4 MI~~i~Il~~~G~~ll~r~y~~~~~--~-~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~Ly~v~v~~~~~n~ 80 (308)
||..++|.|++|+.+++|||.+... + ...+...+.+..+.. ..+.-+........+++++++|||+.+.+...|+
T Consensus 1 mi~FILiqNr~Gk~RLak~yv~~dd~ek~~~~~~vh~lvs~Rd~--K~~~~~~~~~~~~~~~rryagLyf~~~vd~tDne 78 (143)
T KOG0935|consen 1 MIRFILIQNRAGKTRLAKWYVQFDDDEKQKLIEEVHALVTVRDA--KHTNFVEFRNFKIIYRRRYAGLYFCICVDVTDNE 78 (143)
T ss_pred CeEEEEEEccccceeheeeeeccCchHHHHHHHHHHHHHhhccc--hhhhheeeeeceEEEEEeeCCEEEEEEEecCCch
Confidence 8999999999999999999986433 2 244566666665532 1223344555556666799999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhcchhHHHHhhhHHHHHHHHHHHHcCCeeeecChHHHHHHhc
Q 021735 81 ASILLFLHRVADVFKHYFEELEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIK 139 (308)
Q Consensus 81 l~~~~~L~~~~~~l~~y~~~l~e~~I~~n~~~v~~lLDEiid~G~p~~t~~~~L~~~i~ 139 (308)
+..++.+|.|+++|+.||+++||.++..||-.||.++|||+-+|.+++|++..+-+.+.
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 99999999999999999999999999999999999999999999999999987766554
No 11
>KOG2677 consensus Stoned B synaptic vesicle biogenesis protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.81 E-value=8.8e-21 Score=183.41 Aligned_cols=132 Identities=30% Similarity=0.516 Sum_probs=116.1
Q ss_pred CccccceEEEEEEEeEeEEEccCCcEEEEEEEEEEEEEEEeCCCCeEEEeeccchhhhhcc-------CCCCCceeeccc
Q 021735 166 IRYKKNEVFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQG-------RSTKGKAIDLDD 238 (308)
Q Consensus 166 ~~~~~nei~vdv~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~-------~~~~~~~~~l~~ 238 (308)
..|..+||.|||.++.+++++++|.++...|..+|.|.|||+|.|+|.|||||..+.++.- +.....|++|.+
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 4689999999999999999999999999999999999999999999999999998755431 123578999999
Q ss_pred ccccccccccCccCCCeEEEeCCCC-ceEEEEEEecCC-CCCcEEEEEEEEEcCceEEEEEE
Q 021735 239 IKFHQCVRLARFENDRTISFIPPDG-SFDLMTYRLSTQ-VKPLIWVEAQIERHSRSRIEIMV 298 (308)
Q Consensus 239 ~~fH~cV~~~~f~~~~~i~F~PPdg-~f~Lm~Y~~~~~-~~~P~~v~~~~~~~~~~~~~~~i 298 (308)
|.||.|||.++|+++|+|.|.|||| .|+||+||+..+ ..+||+++..+...| .+||+.+
T Consensus 662 ~~FH~cVn~~eF~~srVI~F~PlDaCrFElMRFrt~~~~~~lpftlks~~~V~G-a~VEvq~ 722 (922)
T KOG2677|consen 662 CRFHGCVNEDEFHNSRVILFNPLDACRFELMRFRTVFAEKTLPFTLKSATSVNG-AEVEVQS 722 (922)
T ss_pred eeeecccchhhccccceEEecCcccceeeeeeeeeecCCCcCceeeeeeeeecc-ceeehHH
Confidence 9999999999999999999999999 799999999754 489999988887754 4566643
No 12
>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.78 E-value=4.2e-18 Score=139.27 Aligned_cols=139 Identities=16% Similarity=0.292 Sum_probs=126.1
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCCh--hHHHHHHHHhccccCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCHH
Q 021735 4 AASALFLLDIKGRVLIWRDYRGDVSA--IQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAA 81 (308)
Q Consensus 4 MI~~i~Il~~~G~~ll~r~y~~~~~~--~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~Ly~v~v~~~~~n~l 81 (308)
.+++++|+|++|++++.|||.++.+. ....+|.+.+.++... +...|..++|..++|+..-+|+|..+...++|++
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 36899999999999999999987765 2456899999876532 4578999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhcc-hhHHHHhhhHHHHHHHHHHHHcCCeeeecChHHHHHHhcccccc
Q 021735 82 SILLFLHRVADVFKHYFEE-LEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYR 144 (308)
Q Consensus 82 ~~~~~L~~~~~~l~~y~~~-l~e~~I~~n~~~v~~lLDEiid~G~p~~t~~~~L~~~i~~~~~~ 144 (308)
+..+.|+.+.+.+.-.+.+ +....+.+|++.+...+||+||+|.+++||++++...+...+..
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 9999999999999999987 89999999999999999999999999999999999999877654
No 13
>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=99.33 E-value=6.9e-12 Score=102.57 Aligned_cols=139 Identities=16% Similarity=0.214 Sum_probs=118.8
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCChh----------HHHHHHHHhccccCCCCCCCCEEEeCCEEEEEEEeCCEEEEEE
Q 021735 4 AASALFLLDIKGRVLIWRDYRGDVSAI----------QAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAA 73 (308)
Q Consensus 4 MI~~i~Il~~~G~~ll~r~y~~~~~~~----------~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~Ly~v~v 73 (308)
.+.|++|+|++|++++.|||.+..... ....|.+.+..+.. .+...|..+++..++|++..++.++.+
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 DVEALLILDSQGERIYRKYYQPPHRSEGHQLVFNSVKKEKEFEKKLAEKTA--KDRESILMFYDRLVMCKRLDDVLLYIV 84 (187)
T ss_pred eeeeeEEecCCccchhhhhcCCcccccccchhhcchhHHHHHHHHHHHHhh--cCccceeeEcceeeeeeeehhEEEEEe
Confidence 368999999999999999998643211 34478888865431 134689999999999999999999999
Q ss_pred ecCCCCHHHHHHHHHHHHHHHHHHhcc-hhHHHHhhhHHHHHHHHHHHHcCCeeeecChHHHHHHhcccccc
Q 021735 74 SRQNCNAASILLFLHRVADVFKHYFEE-LEEESLRDNFVVVYELLDEIMDFGFPQFTEAKILSEFIKTDAYR 144 (308)
Q Consensus 74 ~~~~~n~l~~~~~L~~~~~~l~~y~~~-l~e~~I~~n~~~v~~lLDEiid~G~p~~t~~~~L~~~i~~~~~~ 144 (308)
..-++|+.++.+.+..|..+|.-.++. .++..+.+|||.+..+.||.||.|.+.+|+++.+.+.++.++..
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 999999999999999999999999998 56666999999999999999999999999999999999876543
No 14
>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=96.57 E-value=0.025 Score=55.27 Aligned_cols=90 Identities=12% Similarity=0.134 Sum_probs=61.3
Q ss_pred eEEEEEcCCCCEEEEEccCCCCCh---hHHHHHHHHhccccCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCHHH
Q 021735 6 SALFLLDIKGRVLIWRDYRGDVSA---IQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAAS 82 (308)
Q Consensus 6 ~~i~Il~~~G~~ll~r~y~~~~~~---~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~Ly~v~v~~~~~n~l~ 82 (308)
+.+||+++.||++++|+=.++.-. +.+.++..-+.... +.---+..+++.+++..++.||+||+++..+++..
T Consensus 12 kh~fIlS~AGKPIysr~G~e~~l~~~~g~~~aiiS~~~~~~----d~l~~i~~~~~~ivfl~r~pl~lv~vS~~~e~~~~ 87 (415)
T PF03164_consen 12 KHFFILSSAGKPIYSRYGDEDKLSSLMGVIQAIISFFQSNG----DELRSIRAGDHRIVFLNRGPLILVAVSKTGESESQ 87 (415)
T ss_pred CeEEEECCCCceeEEecCChHHHHHHHHHHHHHHHHHHhCC----CcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCHHH
Confidence 479999999999999883221111 23334433332221 12235567899999999999999999999999877
Q ss_pred HHHHHHHHHHHHHHHhc
Q 021735 83 ILLFLHRVADVFKHYFE 99 (308)
Q Consensus 83 ~~~~L~~~~~~l~~y~~ 99 (308)
+..-|+.+...+-..+.
T Consensus 88 l~~qL~~ly~qils~lt 104 (415)
T PF03164_consen 88 LRKQLDYLYSQILSILT 104 (415)
T ss_pred HHHHHHHHHHHHHHhcc
Confidence 77666666666555544
No 15
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=94.98 E-value=0.26 Score=42.74 Aligned_cols=80 Identities=8% Similarity=0.045 Sum_probs=70.4
Q ss_pred CEEEEEEEeCCEEEEEEecCCCCHHHHHHHHHHHHHHHHHHhcchh-HHHHhhhHHHHHHHHHHHHcCCeeeecChHHHH
Q 021735 57 GVTYMFIQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFEELE-EESLRDNFVVVYELLDEIMDFGFPQFTEAKILS 135 (308)
Q Consensus 57 ~~~~v~~~~~~Ly~v~v~~~~~n~l~~~~~L~~~~~~l~~y~~~l~-e~~I~~n~~~v~~lLDEiid~G~p~~t~~~~L~ 135 (308)
...+++....++-|..+++..+|-+++-.+|..++..|.+.+..++ ...+...-+.|..+|+..++.|.-.-.+-+.++
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 3688999999999999999999999999999999999999997643 366778999999999999999998887776555
Q ss_pred H
Q 021735 136 E 136 (308)
Q Consensus 136 ~ 136 (308)
.
T Consensus 183 ~ 183 (189)
T PF15001_consen 183 Q 183 (189)
T ss_pred H
Confidence 4
No 16
>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=94.21 E-value=0.76 Score=36.95 Aligned_cols=92 Identities=11% Similarity=0.129 Sum_probs=62.5
Q ss_pred eeEEEEEcCCCCEEEEEccCCCCCh----hHHHHHHHHhccccC--CCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCC
Q 021735 5 ASALFLLDIKGRVLIWRDYRGDVSA----IQAERFFTKFIEKEG--DPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNC 78 (308)
Q Consensus 5 I~~i~Il~~~G~~ll~r~y~~~~~~----~~~~~f~~~i~~~~~--~~~~~~pii~~~~~~~v~~~~~~Ly~v~v~~~~~ 78 (308)
+.+++|.|++|=+++.-...+.... ..+..|-....+.++ -+....-+..++++.+++.....+|+..+++.+.
T Consensus 17 l~~I~itDrDGvpi~~v~~~~~~~~~~~~~~~~tf~~a~~Q~~KL~lG~nk~ii~~Y~~~qvv~~~~~pl~it~ias~~a 96 (119)
T PF08923_consen 17 LQAIVITDRDGVPIAKVSSDSAPESAMRPSLLSTFAMAIDQASKLGLGKNKSIIAYYDSYQVVQFNKLPLYITFIASSNA 96 (119)
T ss_dssp EEEEEEEETTS-EEEEEE-TTS-GGGGSHHHHCCHHHHHHHHTTSSS-SEEEEEEEESSEEEEEEEETTEEEEEEEETTS
T ss_pred eEEEEEECCCCcEEEEecCCCCcchhhhhHHHHHHHHHhhcccccCCCCceEEEEEeCCEEEEEEeCCCeEEEEEecCCC
Confidence 6899999999999988444432111 122234433333222 1112234667899999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHHHH
Q 021735 79 NAASILLFLHRVADVFKH 96 (308)
Q Consensus 79 n~l~~~~~L~~~~~~l~~ 96 (308)
|.-.++.+-+.+..++++
T Consensus 97 N~G~il~l~~~L~~~l~~ 114 (119)
T PF08923_consen 97 NTGLILSLEEELAPILNE 114 (119)
T ss_dssp -HHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHhHHHHHHHHHH
Confidence 999999999998888875
No 17
>KOG0997 consensus Uncharacterized conserved protein Sand [Function unknown]
Probab=93.79 E-value=0.58 Score=45.88 Aligned_cols=75 Identities=20% Similarity=0.274 Sum_probs=52.0
Q ss_pred eEEEEEcCCCCEEEEEccCCCCCh---hHHHHHHHHhccccCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCHHH
Q 021735 6 SALFLLDIKGRVLIWRDYRGDVSA---IQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAAS 82 (308)
Q Consensus 6 ~~i~Il~~~G~~ll~r~y~~~~~~---~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~Ly~v~v~~~~~n~l~ 82 (308)
+.+||+.+.|+++++|+-..+... +..++...-+...+ ..-..+...|..+++.+.+.|++||+++.+..+..
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 468999999999999986643321 23333333332221 12345678999999999999999999998777655
Q ss_pred HH
Q 021735 83 IL 84 (308)
Q Consensus 83 ~~ 84 (308)
..
T Consensus 194 L~ 195 (523)
T KOG0997|consen 194 LL 195 (523)
T ss_pred HH
Confidence 43
No 18
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=93.70 E-value=1.6 Score=34.55 Aligned_cols=89 Identities=15% Similarity=0.309 Sum_probs=56.7
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCCh----------h---HHHHHHHHhccccCCCCCCCC--EEEeCC-EEEEEEEeCC
Q 021735 4 AASALFLLDIKGRVLIWRDYRGDVSA----------I---QAERFFTKFIEKEGDPQSQNP--VVFDNG-VTYMFIQHNN 67 (308)
Q Consensus 4 MI~~i~Il~~~G~~ll~r~y~~~~~~----------~---~~~~f~~~i~~~~~~~~~~~p--ii~~~~-~~~v~~~~~~ 67 (308)
.+.++||+|+.|-.+++|.|.++... + -..++..++.... + .++ ++..+. +-.+|+...+
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 57999999999999999999765432 0 1112222222211 1 122 344443 5677888889
Q ss_pred EEEEEEe-cCCCCHHHHHHHHHHHHHHHHHHhc
Q 021735 68 VYLMAAS-RQNCNAASILLFLHRVADVFKHYFE 99 (308)
Q Consensus 68 Ly~v~v~-~~~~n~l~~~~~L~~~~~~l~~y~~ 99 (308)
+-||+++ +...|.++- |+++..+..+|.-
T Consensus 78 ~kFV~~~~k~t~na~~q---l~kiY~lYsdYV~ 107 (134)
T COG5122 78 TKFVFVAEKRTVNALFQ---LQKIYSLYSDYVT 107 (134)
T ss_pred cEEEEEecCCchhHHHH---HHHHHHHHHHHhh
Confidence 9999998 444565443 6778888888764
No 19
>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=93.04 E-value=6 Score=36.08 Aligned_cols=115 Identities=13% Similarity=0.181 Sum_probs=62.0
Q ss_pred EEEEEEEeEeEEEccCCcEEEEEEEEEEEEEEEeCC------CCeEEEeeccchhhhhccCCCCCceeeccccccccccc
Q 021735 173 VFLDVVESVNILVNSNGQIVRSDVVGALKMRTYLSG------MPECKLGLNDRVLLEAQGRSTKGKAIDLDDIKFHQCVR 246 (308)
Q Consensus 173 i~vdv~E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG------~P~~~l~ln~~~~~~~~~~~~~~~~~~l~~~~fH~cV~ 246 (308)
+-..|.|.|||.+.. |.+.++.|.|+|.+.---.- .+.+.+.|++...+ +.+.-.+..=
T Consensus 3 l~asi~E~VnA~Fk~-g~~~~v~v~GEv~ls~~~~~~~~~~~~~~l~~rl~n~~~l--------------e~i~pN~~~v 67 (257)
T PF10291_consen 3 LNASITETVNAYFKG-GQLSKVKVTGEVALSYPAGISSSLTSPPPLSFRLNNFSRL--------------EKIAPNPQFV 67 (257)
T ss_dssp EEEEEEEEEEEEEET-TEEEEEEEEEEEEEEEE--SSS-----SEEEEEEETGGGE--------------EEEEE-TTTE
T ss_pred eeEEEEEEEEEEEEC-CcEEEEEEEEEEEEecCCChhhcccCCCcEEEEEcCcchh--------------ceeecCHhHe
Confidence 456799999999964 78889999999988643322 34677888765432 2211111110
Q ss_pred ccCccCCCeEEEeCCC--Cce--EEEEEEecCC----CCCcEEEEEEEEEcCceEEEEEEEEeec
Q 021735 247 LARFENDRTISFIPPD--GSF--DLMTYRLSTQ----VKPLIWVEAQIERHSRSRIEIMVKARSQ 303 (308)
Q Consensus 247 ~~~f~~~~~i~F~PPd--g~f--~Lm~Y~~~~~----~~~P~~v~~~~~~~~~~~~~~~i~l~~~ 303 (308)
...-.++....|.++. ... ..++|++... ..+|+.+.+.-+-. ..+.++.|.++.+
T Consensus 68 ~~~~~~~~~f~~n~~~l~~~~~~~alKYqv~~~~~~~~~~Pl~l~~~Wk~e-~~~tsl~l~Y~~N 131 (257)
T PF10291_consen 68 SSSSQSDGEFWLNMSALTSHLPKQALKYQVHSDPSNLSSVPLILKPVWKCE-PSQTSLILDYKLN 131 (257)
T ss_dssp --EEEETTEEEE-TTTTBT-E-EEEEEEEEES--------SEEEEEEEEE--SSEEEEEEEEEE-
T ss_pred ecCCCCCCcEEEehHHhhhhhhhceEEEEEeccccccCCCCeEEEeEEEeC-CceEEEEEEEEeC
Confidence 0000112234444433 223 5699999753 57899887765543 3455666655543
No 20
>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=92.85 E-value=4.2 Score=33.60 Aligned_cols=93 Identities=10% Similarity=0.198 Sum_probs=54.0
Q ss_pred eeEEEEEcCCCCEEEEEccCCCC----Ch---h----------HHHHHHHHhccccCCC--CCCCC--EEEeCCEEEE-E
Q 021735 5 ASALFLLDIKGRVLIWRDYRGDV----SA---I----------QAERFFTKFIEKEGDP--QSQNP--VVFDNGVTYM-F 62 (308)
Q Consensus 5 I~~i~Il~~~G~~ll~r~y~~~~----~~---~----------~~~~f~~~i~~~~~~~--~~~~p--ii~~~~~~~v-~ 62 (308)
|.++||+|+.|.++++|.|.... ++ . .+.+|..++....... ..... .++.+..... |
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 67999999999999999998643 11 1 2224444444321110 00112 4456666544 4
Q ss_pred EEeCCEEEEEEecCCCCHHHHHHHHHHHHHHHHHHh
Q 021735 63 IQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYF 98 (308)
Q Consensus 63 ~~~~~Ly~v~v~~~~~n~l~~~~~L~~~~~~l~~y~ 98 (308)
....++-||++++.+... ..=++++.+.++.-+|.
T Consensus 81 eT~TGlKFvl~td~~~~~-~~~~l~~~~~~lY~dyV 115 (142)
T PF04099_consen 81 ETPTGLKFVLITDPNVPS-LRDELLRIYYELYVDYV 115 (142)
T ss_dssp E-TTS-EEEEEE-TTCCH-CHHHHHHHHHHHHHHHH
T ss_pred EcCcCcEEEEEecCCCcc-HHHHHHHHHHHHHHHHH
Confidence 556789999999988754 34457888888888876
No 21
>PF13774 Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3BW6_A 1H8M_A 3EGX_C 2NUP_C 3EGD_C 2NUT_C 3KYQ_A 1IFQ_B 2VX8_D ....
Probab=92.62 E-value=0.94 Score=33.54 Aligned_cols=49 Identities=6% Similarity=0.210 Sum_probs=43.4
Q ss_pred CEEEeCCEEEEEEEeCCEEEEEEecCCCCHHHHHHHHHHHHHHHHHHhc
Q 021735 51 PVVFDNGVTYMFIQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFE 99 (308)
Q Consensus 51 pii~~~~~~~v~~~~~~Ly~v~v~~~~~n~l~~~~~L~~~~~~l~~y~~ 99 (308)
-.++.++..|.+...+++.++|+++.+-+.-.++.||+.+.+-...-++
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 4677889999998899999999999999999999999999998888777
No 22
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.00 E-value=2.7 Score=36.66 Aligned_cols=89 Identities=12% Similarity=0.231 Sum_probs=63.4
Q ss_pred EEEEcCCCCEEEEEccCCCCC-hhHHHHHHHHhccccCCCCCCCCEEEeCCEEEEEEEeCCEEEEEEecCCCCHHHHHHH
Q 021735 8 LFLLDIKGRVLIWRDYRGDVS-AIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNNVYLMAASRQNCNAASILLF 86 (308)
Q Consensus 8 i~Il~~~G~~ll~r~y~~~~~-~~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~Ly~v~v~~~~~n~l~~~~~ 86 (308)
+|=+=.+|.++++++-.-... .+..+....++... ++..--..+|++.|-|.+.+++.++|+++.+..-..++.|
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 334447999999976432122 23444444444432 1224467789999999999999999999988888889999
Q ss_pred HHHHHHHHHHHhcc
Q 021735 87 LHRVADVFKHYFEE 100 (308)
Q Consensus 87 L~~~~~~l~~y~~~ 100 (308)
|+++.+=+..-+|.
T Consensus 80 Le~Ik~~F~k~YG~ 93 (217)
T KOG0859|consen 80 LERIKEDFKKRYGG 93 (217)
T ss_pred HHHHHHHHHHHhcc
Confidence 99998877776665
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=88.67 E-value=7.8 Score=31.87 Aligned_cols=73 Identities=18% Similarity=0.252 Sum_probs=37.7
Q ss_pred ceeEEEEEcCCCCEEEEEccCCC-CChhHHHHHHHHhccccCCCC---CCCCEEEe-------CCEEEEEEEe--CCEEE
Q 021735 4 AASALFLLDIKGRVLIWRDYRGD-VSAIQAERFFTKFIEKEGDPQ---SQNPVVFD-------NGVTYMFIQH--NNVYL 70 (308)
Q Consensus 4 MI~~i~Il~~~G~~ll~r~y~~~-~~~~~~~~f~~~i~~~~~~~~---~~~pii~~-------~~~~~v~~~~--~~Ly~ 70 (308)
|++++.|++.+|+++++..=-+. .....+.+|..++++.+.... ...-+..+ ++..++|.-. -.|||
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 99999999999999999433221 112466789999987542111 11223333 3566555433 47999
Q ss_pred EEEecC
Q 021735 71 MAASRQ 76 (308)
Q Consensus 71 v~v~~~ 76 (308)
|++-..
T Consensus 81 VvTyae 86 (148)
T PF09201_consen 81 VVTYAE 86 (148)
T ss_dssp EEEESS
T ss_pred EEEecc
Confidence 988765
No 24
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=87.59 E-value=8.5 Score=38.26 Aligned_cols=114 Identities=15% Similarity=0.125 Sum_probs=72.8
Q ss_pred ceeEEEEEcCCCCEEEEEccCCCCChhHHHHHHHHhccccCCCCCCCCEEEeCCEEEEEEEeCC--EEEEEEecCCCCHH
Q 021735 4 AASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVTYMFIQHNN--VYLMAASRQNCNAA 81 (308)
Q Consensus 4 MI~~i~Il~~~G~~ll~r~y~~~~~~~~~~~f~~~i~~~~~~~~~~~pii~~~~~~~v~~~~~~--Ly~v~v~~~~~n~l 81 (308)
||+.|.|+++.|-+|..+.=.++.-...+.+|.+.++..... +... +..+.++.=|...|+ +.|+++-..--+-.
T Consensus 1 Mld~faIFtkgG~vLw~~~~~~~~~~~~in~lI~~~ll~er~-~~~~--~~~~~yTlk~q~~N~~~lvfvvvfqki~~L~ 77 (587)
T KOG0781|consen 1 MLDQFAIFTKGGLVLWCYQEVGDNLKGPINALIRSVLLSERG-GVNS--FTFEAYTLKYQLDNQYSLVFVVVFQKILTLT 77 (587)
T ss_pred CcceeeeecCCcEEEEEecccchhccchHHHHHHHHHHHhhc-Cccc--CchhheeEeeeecCCccEEEEEEEeccchhh
Confidence 899999999999999884433332233456666666543211 1111 555666666666665 66667666555666
Q ss_pred HHHHHHHHHHHHHHHHhcchhHHHHhhhHH-HHHHHHHHH
Q 021735 82 SILLFLHRVADVFKHYFEELEEESLRDNFV-VVYELLDEI 120 (308)
Q Consensus 82 ~~~~~L~~~~~~l~~y~~~l~e~~I~~n~~-~v~~lLDEi 120 (308)
.+-.+|....+...+-|...+...++.|++ ...++|++-
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 677777777777777777766777777755 455555543
No 25
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=82.67 E-value=19 Score=30.79 Aligned_cols=46 Identities=9% Similarity=0.192 Sum_probs=34.8
Q ss_pred EEEeCC-EEEEEEEeCCEEEEEEecCCCCHHHHHHHHHHHHHHHHHHhc
Q 021735 52 VVFDNG-VTYMFIQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFE 99 (308)
Q Consensus 52 ii~~~~-~~~v~~~~~~Ly~v~v~~~~~n~l~~~~~L~~~~~~l~~y~~ 99 (308)
+++.+. .-++|+..-++=||++++... ..+=.+|.++.++..+|.=
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 467888999999999988765 3455688999999999863
No 26
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=66.06 E-value=85 Score=27.85 Aligned_cols=49 Identities=10% Similarity=0.249 Sum_probs=43.9
Q ss_pred EEEeCCEEEEEEEeCCEEEEEEecCCCCHHHHHHHHHHHHHHHHHHhcc
Q 021735 52 VVFDNGVTYMFIQHNNVYLMAASRQNCNAASILLFLHRVADVFKHYFEE 100 (308)
Q Consensus 52 ii~~~~~~~v~~~~~~Ly~v~v~~~~~n~l~~~~~L~~~~~~l~~y~~~ 100 (308)
-++.+...|.|...+++.+.+.++.+-+--+++.+|+.+.+-+..-++.
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 4567789999999999999999999999999999999999988887775
No 27
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=59.75 E-value=96 Score=25.39 Aligned_cols=90 Identities=11% Similarity=0.253 Sum_probs=50.3
Q ss_pred cceeEEEEEcCCCCEEEEEccCCCCC----hh-----------HHHHHHHHhccccCCCCCCCCEEE--eCCEEEEEEEe
Q 021735 3 GAASALFLLDIKGRVLIWRDYRGDVS----AI-----------QAERFFTKFIEKEGDPQSQNPVVF--DNGVTYMFIQH 65 (308)
Q Consensus 3 ~MI~~i~Il~~~G~~ll~r~y~~~~~----~~-----------~~~~f~~~i~~~~~~~~~~~pii~--~~~~~~v~~~~ 65 (308)
+.|.+++|+|++|.+++.+.|..... +. .+..|.+++..... ...+.. .......|...
T Consensus 1 Mtiy~~yIFdR~g~Cl~y~EW~r~~~s~~~~eee~KL~yGmlFSlkS~v~Kls~~d~----k~~f~sy~Ts~YklhfyeT 76 (140)
T KOG3368|consen 1 MTIYNFYIFDRNGVCLFYREWNRTKQSGIPNEEEAKLMYGMLFSLKSFVSKLSPGDV----KDGFLSYKTSKYKLHFYET 76 (140)
T ss_pred CeEEEEEEEcCCccEEEehhcccccccCCchhHHHHHHHHHHhhHHHHHHhcCCCCc----ccCeeEEeeceeEEEEEEc
Confidence 45889999999999999987753221 11 11233333332211 112332 33444444333
Q ss_pred -CCEEEEEEecCCCCHHHHHHHHHHHHH-HHHHHh
Q 021735 66 -NNVYLMAASRQNCNAASILLFLHRVAD-VFKHYF 98 (308)
Q Consensus 66 -~~Ly~v~v~~~~~n~l~~~~~L~~~~~-~l~~y~ 98 (308)
.+|.||..++..... +=+.||.|.. +--+|.
T Consensus 77 ptglk~vl~Tdpk~~~--ir~vLq~IYs~lyVE~V 109 (140)
T KOG3368|consen 77 PTGLKFVLNTDPKAGS--IRDVLQYIYSHLYVEYV 109 (140)
T ss_pred CCCcEEEEecCCCccc--HHHHHHHHHHHHHHHHH
Confidence 579999999877643 3455666665 434443
No 28
>KOG0647 consensus mRNA export protein (contains WD40 repeats) [RNA processing and modification]
Probab=30.24 E-value=1.5e+02 Score=27.98 Aligned_cols=89 Identities=18% Similarity=0.216 Sum_probs=59.1
Q ss_pred EeEeEEEccCCcEEEEEEEEEEEEEEEeCCCCeEEEeeccchhhhhccCCCCCceeeccccccccccc-ccCccCCCeEE
Q 021735 179 ESVNILVNSNGQIVRSDVVGALKMRTYLSGMPECKLGLNDRVLLEAQGRSTKGKAIDLDDIKFHQCVR-LARFENDRTIS 257 (308)
Q Consensus 179 E~i~~~~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~l~~~~fH~cV~-~~~f~~~~~i~ 257 (308)
-.|.+.-+++|. ....|.|++.+..--.|+|.-.+.|.-....+ .....-.-+.++.|||--. +..-.++.+.+
T Consensus 202 R~va~f~d~~~~-alGsiEGrv~iq~id~~~~~~nFtFkCHR~~~----~~~~~VYaVNsi~FhP~hgtlvTaGsDGtf~ 276 (347)
T KOG0647|consen 202 RCVACFQDKDGF-ALGSIEGRVAIQYIDDPNPKDNFTFKCHRSTN----SVNDDVYAVNSIAFHPVHGTLVTAGSDGTFS 276 (347)
T ss_pred eEEEEEecCCce-EeeeecceEEEEecCCCCccCceeEEEeccCC----CCCCceEEecceEeecccceEEEecCCceEE
Confidence 356777888888 77889999999999999997777775442111 0111123467899999221 12333567788
Q ss_pred EeCCCCceEEEEEEe
Q 021735 258 FIPPDGSFDLMTYRL 272 (308)
Q Consensus 258 F~PPdg~f~Lm~Y~~ 272 (308)
|-.-|.+-.|..|..
T Consensus 277 FWDkdar~kLk~s~~ 291 (347)
T KOG0647|consen 277 FWDKDARTKLKTSET 291 (347)
T ss_pred EecchhhhhhhccCc
Confidence 877777777777664
No 29
>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=27.61 E-value=2.9e+02 Score=21.40 Aligned_cols=87 Identities=9% Similarity=0.116 Sum_probs=49.6
Q ss_pred eeEEEEEcCCCCEEEEEccCCCCChhHHHHHHHHhccccCCCCCCCCEEEeCCEE-------------------EEEEEe
Q 021735 5 ASALFLLDIKGRVLIWRDYRGDVSAIQAERFFTKFIEKEGDPQSQNPVVFDNGVT-------------------YMFIQH 65 (308)
Q Consensus 5 I~~i~Il~~~G~~ll~r~y~~~~~~~~~~~f~~~i~~~~~~~~~~~pii~~~~~~-------------------~v~~~~ 65 (308)
+.+..|++.+|.+..+.---...+...+..+.+.+..... ....-+.++|.. ++-.+.
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 ITKAAIIGSDGSVWASSPGFSNISPEEAKAIIKAFNNPSK---FPSNGITLGGKKYIVLRADDNSIYGKKGKGGIIIVKT 92 (121)
T ss_dssp ESEEEEEETTSSEEEEETTGGGCSHHHHHHHHHHHHSSSH---HHHH-EEETTEEEEEEEEETTEEEEEETTEEEEEEEC
T ss_pred EeEEEEEcCCCCEEEecCCCCCCCHHHHHHHHHHhcCchh---cccCCeEEcCcEeEEEecCCceEEeeCCCCcEEEEEC
Confidence 6677888899987776432101222333344443332210 001123333333 344444
Q ss_pred CCEEEEEEecCCCCHHHHHHHHHHHHHHH
Q 021735 66 NNVYLMAASRQNCNAASILLFLHRVADVF 94 (308)
Q Consensus 66 ~~Ly~v~v~~~~~n~l~~~~~L~~~~~~l 94 (308)
+..++|+..+.+.+|-.+.....++++.|
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 56788888888899999988888888765
No 30
>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=23.39 E-value=3.9e+02 Score=21.40 Aligned_cols=21 Identities=38% Similarity=0.589 Sum_probs=16.8
Q ss_pred eeEEEEEcCCCCEEE--EEccCC
Q 021735 5 ASALFLLDIKGRVLI--WRDYRG 25 (308)
Q Consensus 5 I~~i~Il~~~G~~ll--~r~y~~ 25 (308)
+++++++|.+|++++ .+.+..
T Consensus 50 ~d~~~~~d~~g~~~~~~~~~~~~ 72 (161)
T PF05228_consen 50 LDLIFILDPDGRVLYSSSKGYDF 72 (161)
T ss_pred ccEEEEEcCCCCEEEEeccCccc
Confidence 578999999999999 555443
No 31
>COG3322 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]
Probab=23.26 E-value=90 Score=29.16 Aligned_cols=36 Identities=11% Similarity=0.246 Sum_probs=26.1
Q ss_pred eeEEEEEcCCCCEEEEEccCCCCChh--HHHHHHHHhc
Q 021735 5 ASALFLLDIKGRVLIWRDYRGDVSAI--QAERFFTKFI 40 (308)
Q Consensus 5 I~~i~Il~~~G~~ll~r~y~~~~~~~--~~~~f~~~i~ 40 (308)
++.+|++|.+|++++++.+....... ..+.+.+.+.
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 46899999999999999996543322 3356666655
No 32
>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=21.81 E-value=1.1e+02 Score=20.04 Aligned_cols=18 Identities=44% Similarity=0.658 Sum_probs=14.0
Q ss_pred EEeCCCCceEEEEEEecC
Q 021735 257 SFIPPDGSFDLMTYRLST 274 (308)
Q Consensus 257 ~F~PPdg~f~Lm~Y~~~~ 274 (308)
.|---||.|+.|.|.-+.
T Consensus 15 vfpn~dgtftamtytksk 32 (49)
T PF07151_consen 15 VFPNQDGTFTAMTYTKSK 32 (49)
T ss_pred EeeCCCCcEEEEEEeecc
Confidence 355568999999999654
No 33
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=21.59 E-value=1.3e+02 Score=22.89 Aligned_cols=23 Identities=22% Similarity=-0.067 Sum_probs=18.7
Q ss_pred hhHHHHHHHHHHHHcCCeeeecC
Q 021735 108 DNFVVVYELLDEIMDFGFPQFTE 130 (308)
Q Consensus 108 ~n~~~v~~lLDEiid~G~p~~t~ 130 (308)
-+-..|...++++++.|+++.|-
T Consensus 77 ~~~~~v~~al~~L~~eG~IYsTi 99 (102)
T PF08784_consen 77 MSENEVRKALDFLSNEGHIYSTI 99 (102)
T ss_dssp S-HHHHHHHHHHHHHTTSEEESS
T ss_pred cCHHHHHHHHHHHHhCCeEeccc
Confidence 34567889999999999999874
No 34
>KOG0283 consensus WD40 repeat-containing protein [Function unknown]
Probab=20.33 E-value=1.3e+02 Score=31.61 Aligned_cols=36 Identities=19% Similarity=0.109 Sum_probs=28.3
Q ss_pred EeEeEE-EccCCcEEEEEEEEEEEEEEEeCCCCeEEEee
Q 021735 179 ESVNIL-VNSNGQIVRSDVVGALKMRTYLSGMPECKLGL 216 (308)
Q Consensus 179 E~i~~~-~~~~G~i~~~~v~G~i~~~s~LsG~P~~~l~l 216 (308)
+.|+|+ +++. -.+.-|.|+|..|++|=+.|++++..
T Consensus 410 dfVTcVaFnPv--DDryFiSGSLD~KvRiWsI~d~~Vv~ 446 (712)
T KOG0283|consen 410 DFVTCVAFNPV--DDRYFISGSLDGKVRLWSISDKKVVD 446 (712)
T ss_pred CeeEEEEeccc--CCCcEeecccccceEEeecCcCeeEe
Confidence 456665 6653 45788999999999999999999876
No 35
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=20.31 E-value=92 Score=17.16 Aligned_cols=18 Identities=28% Similarity=0.514 Sum_probs=14.7
Q ss_pred hhHHHHHHHHHHHHcCCe
Q 021735 108 DNFVVVYELLDEIMDFGF 125 (308)
Q Consensus 108 ~n~~~v~~lLDEiid~G~ 125 (308)
.+++.+.+++++|.+.|.
T Consensus 14 ~~~~~a~~~~~~M~~~g~ 31 (31)
T PF01535_consen 14 GQFEEALEVFDEMRERGI 31 (31)
T ss_pred chHHHHHHHHHHHhHCcC
Confidence 567788899999998874
Done!