Query 025655
Match_columns 250
No_of_seqs 124 out of 828
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 08:06:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025655.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025655hhsearch_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 1.6E-70 3.5E-75 483.7 20.1 249 1-250 65-341 (446)
2 KOG0937 Adaptor complexes medi 100.0 4.5E-61 9.8E-66 438.6 20.7 250 1-250 66-317 (424)
3 KOG2740 Clathrin-associated pr 100.0 2.6E-52 5.6E-57 371.0 19.0 218 1-233 68-300 (418)
4 PF00928 Adap_comp_sub: Adapto 100.0 2.7E-38 5.8E-43 278.9 18.4 155 89-250 1-156 (262)
5 KOG2635 Medium subunit of clat 99.9 1.2E-24 2.5E-29 198.5 17.7 231 1-250 67-417 (512)
6 KOG2677 Stoned B synaptic vesi 99.9 1.9E-24 4.1E-29 204.0 4.3 154 95-250 581-753 (922)
7 PF01217 Clat_adaptor_s: Clath 99.5 2.2E-14 4.8E-19 115.7 6.9 71 1-71 68-138 (141)
8 COG5030 APS2 Clathrin adaptor 98.0 5.5E-06 1.2E-10 65.8 4.3 64 2-65 69-132 (152)
9 KOG0934 Clathrin adaptor compl 98.0 3.7E-06 8E-11 66.6 2.6 60 3-62 70-129 (145)
10 KOG0935 Clathrin adaptor compl 97.7 2.8E-05 6.1E-10 60.3 2.6 61 5-65 73-133 (143)
11 KOG0936 Clathrin adaptor compl 97.2 0.00098 2.1E-08 53.9 6.0 72 1-72 74-145 (182)
12 KOG3343 Vesicle coat complex C 96.7 0.0024 5.1E-08 52.1 4.5 70 4-73 78-148 (175)
13 PF10291 muHD: Muniscin C-term 96.1 0.46 9.9E-06 42.2 15.6 131 103-249 3-151 (257)
14 COG5541 RET3 Vesicle coat comp 85.9 0.72 1.6E-05 37.7 2.8 70 4-73 85-155 (187)
15 PF15001 AP-5_subunit_s1: AP-5 77.7 7.7 0.00017 32.9 6.2 66 2-67 118-184 (189)
16 KOG0647 mRNA export protein (c 48.1 53 0.0011 30.1 5.9 88 110-202 203-291 (347)
17 PF09644 Mg296: Mg296 protein; 34.9 67 0.0014 24.7 3.8 30 17-46 4-33 (121)
18 PRK13696 hypothetical protein; 29.4 82 0.0018 21.8 3.2 24 14-37 26-56 (62)
19 PF13494 DUF4119: Domain of un 28.3 27 0.00058 26.0 0.7 36 166-201 57-96 (96)
20 PF07151 DUF1391: Protein of u 24.6 84 0.0018 20.2 2.4 18 187-204 15-32 (49)
21 PF02334 RTP: Replication term 24.4 96 0.0021 24.1 3.1 32 22-56 39-70 (122)
22 PF08784 RPA_C: Replication pr 23.1 1.2E+02 0.0026 22.3 3.6 21 40-60 79-99 (102)
23 smart00836 DALR_1 DALR anticod 22.2 1.6E+02 0.0036 22.0 4.2 45 7-51 58-107 (122)
24 PF04614 Pex19: Pex19 protein 22.1 1.7E+02 0.0037 25.7 4.8 21 37-57 195-215 (248)
25 cd08339 DED_DEDD-like Death Ef 21.8 1.4E+02 0.003 22.3 3.4 36 17-59 5-40 (97)
26 cd07956 Anticodon_Ia_Arg Antic 21.6 1.6E+02 0.0034 23.5 4.2 48 7-54 93-144 (156)
No 1
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.6e-70 Score=483.68 Aligned_cols=249 Identities=43% Similarity=0.752 Sum_probs=225.8
Q ss_pred CeeecCCCCHHHHHHHHHHHHHHHHHhhcccCHHHHHhhHHHHHHHHHHHhcCCeeeecChhhhhhhhcccccccccc--
Q 025655 1 MTASRQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDAYRMEVT-- 78 (250)
Q Consensus 1 v~~t~~~~n~~~~~e~L~~l~~~l~~y~g~l~e~~i~~n~~~iyelLdE~id~G~p~~t~~~~Lk~~i~~~~~~~~~~-- 78 (250)
|++|++|.|.+.++|||..+..++..|||+++|++|++||.+|||+||||+||||||+|+++.|+.+|..++...+-.
T Consensus 65 vaitksN~Nva~v~eFl~kl~avm~aYfgk~~Eeaiknnf~lI~ElLDemld~G~pqnte~~al~~~is~~~Vrs~g~~l 144 (446)
T KOG0938|consen 65 VAITKSNANVAAVFEFLYKLDAVMNAYFGKDREEAIKNNFVLIYELLDEMLDFGIPQNTEPNALKAQISQKGVRSMGGVL 144 (446)
T ss_pred EEEecCCCchhhHHHHHHHHHHHHHHHhcccchhhhhhceEeHHHHHHHHHhcCCCccCChhHHHhhhhhhhhhcccccc
Confidence 689999999999999999999999999999999999999999999999999999999999999999999987765411
Q ss_pred -------cCC----CCCccccccccccCcccccceEEEEEEEeEEEEEccCCcEEEEEEEEEEEEEEEeCCCCeEEEEec
Q 025655 79 -------QRP----PMAVTNAVSWRSEGIQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLN 147 (250)
Q Consensus 79 -------~~~----~~~~~~~~~wR~~~~~~~~nEi~vdV~E~i~~~~~~~G~i~~~~i~G~I~~~s~LsG~P~~~l~ln 147 (250)
++. +++.+++++||+.|++|+|||+|+||.|+++.+++++|++++++|+|.|.|+++|||||+|++|||
T Consensus 145 s~k~s~~sq~~~~~ssqv~G~i~WRr~Gi~ykknevfldvvErvNlLmS~~GnVLrs~VsG~V~mk~~LSGmPeckfGlN 224 (446)
T KOG0938|consen 145 SSKSSPTSQATELRSSQVTGKIGWRREGIKYKKNEVFLDVVERVNLLMSSDGNVLRSDVSGTVDMKTHLSGMPECKFGLN 224 (446)
T ss_pred CCcCCCCcccccccccccccccccccccceeccceeEeEehheeeeEEcCCCCEEEeecccEEEEEEeccCCcccccccC
Confidence 111 145567899999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhhhc-cC-----------C-CCCcceeccccccccccccccccCCceeEecCCCCceEEEEEEecCCC-cCcEEEE
Q 025655 148 DRILLEAQ-GR-----------S-TKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLNTQV-KPLIWVE 213 (250)
Q Consensus 148 ~~~~~~~~-~~-----------~-~~~~~~~l~d~~fH~cV~~~~~~~~r~i~F~PPdg~F~Lm~Yr~~~~~-~P~~~v~ 213 (250)
|++.+... +. + ++...+.|+||+||+||++++|++++.|+|+||||+|+||+||++.++ +||. +.
T Consensus 225 Dkl~~e~kq~esks~~~n~~~~sks~~g~v~leDc~FHqCV~L~kFn~eh~IsFvPPDGe~ELMkYr~~enInlPFr-V~ 303 (446)
T KOG0938|consen 225 DKLGMESKQSESKSDFGNKNFPSKSGKGSVLLEDCTFHQCVRLDKFNSEHIISFVPPDGEFELMKYRVTENINLPFR-VT 303 (446)
T ss_pred cccceeeccccccccccccCCCcccCCceEEeeccchheeeccccccccceEEEeCCCCceEeEeeeeccCcccceE-ee
Confidence 99877632 11 0 233458999999999999999999999999999999999999999987 8886 57
Q ss_pred EEEEECcceEEEEEEEEeecCCccccc-ceeEEeecCC
Q 025655 214 AQVERHSRSRVEILVKARSQFKERRCS-DINGICIICT 250 (250)
Q Consensus 214 ~~~~~~~~~~~e~~v~l~~~~~~~~~a-~v~i~ip~p~ 250 (250)
|.++..+.+++||++.+++.|+++..| +++++||+|+
T Consensus 304 PiV~el~r~kie~ri~iks~f~~kl~a~~v~~rIPvP~ 341 (446)
T KOG0938|consen 304 PIVTELGRTKIEYRITIKSLFPPKLLAKDVVVRIPVPP 341 (446)
T ss_pred eheecccceeEEEEEEEeccCCchhhhcceEEEecCCC
Confidence 999998889999999999999998888 9999999995
No 2
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=4.5e-61 Score=438.61 Aligned_cols=250 Identities=58% Similarity=1.003 Sum_probs=231.7
Q ss_pred CeeecCCCCHHHHHHHHHHHHHHHHHhhcccCHHHHHhhHHHHHHHHHHHhcCCeeeecChhhhhhhhccccccccc-cc
Q 025655 1 MTASRQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDAYRMEV-TQ 79 (250)
Q Consensus 1 v~~t~~~~n~~~~~e~L~~l~~~l~~y~g~l~e~~i~~n~~~iyelLdE~id~G~p~~t~~~~Lk~~i~~~~~~~~~-~~ 79 (250)
|++++.|+|++.+++||++++.++.+||+.+.|+.+++||.++||+|||+|||||||.|+.+.|++|+.++++..+. +.
T Consensus 66 v~~~~~n~~a~~v~~~l~~~~~v~~~y~~~l~e~si~~n~vlvyElLde~mDFGypQ~t~s~iL~~yi~~~~~~l~~~~~ 145 (424)
T KOG0937|consen 66 VAGTRPNVSAALVLSFLYAVADVFGDYLSELEEESIRDNFVLVYELLDEVMDFGYPQTTDSEILKNYITQKANRLQDAQP 145 (424)
T ss_pred EEEeccCCCHHHHHHHHHHHHHHHHHHhccCCccceecchHHHHHHHHHHhccCCcccchHHHHHHHhcccccceeecCC
Confidence 57789999999999999999999999999999999999999999999999999999999999999999999776543 23
Q ss_pred CCCCCccccccccccCcccccceEEEEEEEeEEEEEccCCcEEEEEEEEEEEEEEEeCCCCeEEEEeccchhhhhccCCC
Q 025655 80 RPPMAVTNAVSWRSEGIQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQGRST 159 (250)
Q Consensus 80 ~~~~~~~~~~~wR~~~~~~~~nEi~vdV~E~i~~~~~~~G~i~~~~i~G~I~~~s~LsG~P~~~l~ln~~~~~~~~~~~~ 159 (250)
+++.+.+++++||+.|++|+|||+|+||+|+++++++++|.++.++|.|+|+|||+|+|||+++|+||+....+..+..+
T Consensus 146 ~~p~avtnavsWrs~gi~~~KnevflDViE~Vs~l~~~~G~vl~s~i~G~I~~k~~LsGmPelrl~ln~~~~~~~~~~~~ 225 (424)
T KOG0937|consen 146 RPPLAVTNAVSWRSEGIYYGKNEVFLDVIESVSLLYDSNGIVLLSEIVGTIKLKCYLSGMPELRLGLNDKVLFDKQGPRS 225 (424)
T ss_pred CCCcccccceeecccccccccceEEEEhhhhhhHhhhcCCcEEEeeeeeEEEEEEEcCCCceeeeecCcccccccccccc
Confidence 67888899999999999999999999999999999999999999999999999999999999999999998877666555
Q ss_pred CCcceeccccccccccccccccCCceeEecCCCCceEEEEEEecCCCcCcEEEEEEEEECcceEEEEEEEEeecCCcccc
Q 025655 160 KGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLNTQVKPLIWVEAQVERHSRSRVEILVKARSQFKERRC 239 (250)
Q Consensus 160 ~~~~~~l~d~~fH~cV~~~~~~~~r~i~F~PPdg~F~Lm~Yr~~~~~~P~~~v~~~~~~~~~~~~e~~v~l~~~~~~~~~ 239 (250)
.+..+.++|++||+||++++|+.+|+|+|+||||+|+||+||.+....|++.+....+.++..++++.+++++.|+++..
T Consensus 226 ~s~~v~ledi~fh~~v~l~~fd~dr~i~FiPPdGeF~Lm~Y~ls~~vkPli~~~~~~~~~~~~ri~i~~K~~~~fk~~~~ 305 (424)
T KOG0937|consen 226 KSKGVELEDIKFHECVRLSRFDNDRTISFIPPDGEFELMRYRLSTHVKPLIWFYQLIEEHSRSRIEVMVKLREQFKSRSS 305 (424)
T ss_pred cCcceEeeecccceeechhhccCCceEEecCCCCceEEEEEEecCCCCCeEEeeeeeeeccceeEEEEEechhhcCCccc
Confidence 55789999999999999999999999999999999999999999988899887665666777899999999999999988
Q ss_pred c-ceeEEeecCC
Q 025655 240 S-DINGICIICT 250 (250)
Q Consensus 240 a-~v~i~ip~p~ 250 (250)
| ++.|.+|+|.
T Consensus 306 a~~v~I~iP~P~ 317 (424)
T KOG0937|consen 306 ANNVEICIPVPD 317 (424)
T ss_pred cceEEEEeeCCC
Confidence 8 8899999994
No 3
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.6e-52 Score=370.97 Aligned_cols=218 Identities=39% Similarity=0.732 Sum_probs=193.4
Q ss_pred CeeecCCCCHHHHHHHHHHHHHHHHHhhcccCHHHHHhhHHHHHHHHHHHhcCCeeeecChhhhhhhhccccccccc---
Q 025655 1 MTASRQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDAYRMEV--- 77 (250)
Q Consensus 1 v~~t~~~~n~~~~~e~L~~l~~~l~~y~g~l~e~~i~~n~~~iyelLdE~id~G~p~~t~~~~Lk~~i~~~~~~~~~--- 77 (250)
|+++..++.|++++|||+|+++++++|||+++|.+|++|+..||||||||+|+|||..||+|.||++|+.++...+.
T Consensus 68 ~~~st~e~pPL~~iefL~rv~dv~~eyFg~~s~~~Ik~N~~vv~ell~emiDnGfpl~tE~NiLke~i~pps~l~~~~~s 147 (418)
T KOG2740|consen 68 CAVSTVETPPLMVIEFLHRVVDVLLEYFGGLSESKIKDNVVVVYELLDEMIDNGFPLVTEPNILKELIPPPSFLSKKFNS 147 (418)
T ss_pred EEEEeccCCChhHHHHHHHHHHHHHHHhcccCHhHhhcceeeHHHHHHHHHHcCCCcccChhHHHhhcCChHHHHHHHhh
Confidence 46788899999999999999999999999999999999999999999999999999999999999999999877632
Q ss_pred -------ccCCCCCccccccccccCcccccceEEEEEEEeEEEEEccCCcEEEEEEEEEEEEEEEeCCCCeEEEEeccch
Q 025655 78 -------TQRPPMAVTNAVSWRSEGIQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRI 150 (250)
Q Consensus 78 -------~~~~~~~~~~~~~wR~~~~~~~~nEi~vdV~E~i~~~~~~~G~i~~~~i~G~I~~~s~LsG~P~~~l~ln~~~ 150 (250)
+.+.|+++.+.+|||+.+.+|.+||.||||.|+++|+++++|..+.++|.|.|.|+|.|+|||++.|.|+++.
T Consensus 148 vTg~~n~~~~lPtg~~s~VPWR~~~~Ky~nNE~yvdvlEeidai~~k~gslv~~eI~g~vd~~~qLsgmPdltlsl~np~ 227 (418)
T KOG2740|consen 148 VTGNSNVSDTLPTGALSNVPWRTAGVKYTNNEAYVDVLEEIDAIVDKKGSLVFGEIQGIVDVCSQLSGMPDLTLSLNNPR 227 (418)
T ss_pred hhccccccccCCCcccccccccccCcccccchhhhhhhheeheEecCCCCEEEEEEEEEEEEEEeecCCCceEEEccCcc
Confidence 2356777888899999999999999999999999999999999999999999999999999999999998763
Q ss_pred hhhhccCCCCCcceeccccccccccccccccCCceeEecCCCCceEEEEEEecCC--C-cCcEEEEEEEEECcce--EEE
Q 025655 151 LLEAQGRSTKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLNTQ--V-KPLIWVEAQVERHSRS--RVE 225 (250)
Q Consensus 151 ~~~~~~~~~~~~~~~l~d~~fH~cV~~~~~~~~r~i~F~PPdg~F~Lm~Yr~~~~--~-~P~~~v~~~~~~~~~~--~~e 225 (250)
.|+|++|||||+.++|++++.|+|+||||+|+||+||++.. . +|.. +.+.+.-.+.. +++
T Consensus 228 --------------~L~dvsfHpcVr~krwe~~~~lsFIPPDGkFrLlsy~v~~~~~v~~pvy-v~~~i~l~~~~~~ri~ 292 (418)
T KOG2740|consen 228 --------------LLGDVSFHPCVRYKRWESHSVLSFIPPDGKFRLLSYRVDAQNQVAIPVY-VKNSISLDSNHQGRIS 292 (418)
T ss_pred --------------ccCCcccccceeecccccccceEEcCCCCcEEEEEEEEehhhccccceE-EeeeeccCCCceEEEE
Confidence 48999999999999999999999999999999999999754 2 6664 57877765433 444
Q ss_pred EEEEEeec
Q 025655 226 ILVKARSQ 233 (250)
Q Consensus 226 ~~v~l~~~ 233 (250)
+.+..+..
T Consensus 293 ~tvg~~~~ 300 (418)
T KOG2740|consen 293 LTVGPKKK 300 (418)
T ss_pred Eecccccc
Confidence 44444433
No 4
>PF00928 Adap_comp_sub: Adaptor complexes medium subunit family; InterPro: IPR008968 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. This entry represents the C-terminal domain of the mu subunit from various clathrin adaptors (AP1, AP2 and AP3) []. The C-teminal domain has an immunoglobulin-like beta-sandwich fold consisting of 9 strands in 2 sheets with a Greek key topology, similar to that found in cytochrome f and certain transcription factors []. The mu subunit regulates the coupling of clathrin lattices with particular membrane proteins by self-phosphorylation via a mechanism that is still unclear []. The mu subunit possesses a highly conserved N-terminal domain of around 230 amino acids, which may be the region of interaction with other AP proteins; a linker region of between 10 and 42 amino acids; and a less well-conserved C-terminal domain of around 190 amino acids, which may be the site of specific interaction with the protein being transported in the vesicle []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 1H6E_A 3L81_A 1W63_V 4EMZ_A 4EN2_A 2VGL_M 3ML6_F 2PR9_A 2JKT_M 1I31_A ....
Probab=100.00 E-value=2.7e-38 Score=278.90 Aligned_cols=155 Identities=39% Similarity=0.760 Sum_probs=127.0
Q ss_pred ccccccCcccccceEEEEEEEeEEEEEccCCcEEEEEEEEEEEEEEEeCCCCeEEEEeccchhhhhccCCCCCcceeccc
Q 025655 89 VSWRSEGIQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQGRSTKGKAIDLDD 168 (250)
Q Consensus 89 ~~wR~~~~~~~~nEi~vdV~E~i~~~~~~~G~i~~~~i~G~I~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~l~d 168 (250)
+|||+.+.+|++|||||||.|+++++++++|.++.++|.|+|+|+++|+|+|+|+|+||+.... ...++.++|
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 5899999999999999999999999999999999999999999999999999999999998432 125678999
Q ss_pred cccccccccccccCCceeEecCCCCceEEEEEEecCCCcCcEEEEEEEEECcceEEEEEEEEeecCCcc-cccceeEEee
Q 025655 169 IKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLNTQVKPLIWVEAQVERHSRSRVEILVKARSQFKER-RCSDINGICI 247 (250)
Q Consensus 169 ~~fH~cV~~~~~~~~r~i~F~PPdg~F~Lm~Yr~~~~~~P~~~v~~~~~~~~~~~~e~~v~l~~~~~~~-~~a~v~i~ip 247 (250)
++||+|||++.|+++|.|+|+||||+|+||+||++....+|+.+.|++...+++++++.++++++++.. ...++.|+||
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 999999999999999999999999999999999988775555679999986677999999999999874 4559999999
Q ss_pred cCC
Q 025655 248 ICT 250 (250)
Q Consensus 248 ~p~ 250 (250)
+|.
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=99.93 E-value=1.2e-24 Score=198.49 Aligned_cols=231 Identities=17% Similarity=0.274 Sum_probs=185.7
Q ss_pred CeeecCCCCHHHHHHHHHHHHHHHHHhhcccCHHHHHhhHHHHHHHHHHHhcCCeeeecChhhhhhhhccccccccccc-
Q 025655 1 MTASRQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDAYRMEVTQ- 79 (250)
Q Consensus 1 v~~t~~~~n~~~~~e~L~~l~~~l~~y~g~l~e~~i~~n~~~iyelLdE~id~G~p~~t~~~~Lk~~i~~~~~~~~~~~- 79 (250)
|.+|+++.|++.++++|+.|.+++..||..+.|..|.+|.+.+...|||++..||..+.+..|+|.|..|++|+++++.
T Consensus 67 vLITtk~SNIleDl~TL~Lfskvipey~~slde~eI~~~~FelifAFDEivsLGyre~v~laQikty~eMdSHEEKi~e~ 146 (512)
T KOG2635|consen 67 VLITTKQSNILEDLETLRLFSKVIPEYCSSLDEKEILENAFELIFAFDEIVSLGYRENVNLAQIKTYLEMDSHEEKIHEL 146 (512)
T ss_pred EEEeccccchhhHHHHHHHHHHhchhhhhhhhHHHHHHhhhhhhhccchhhhhcccccccHHHhhhhhccccHHHHHHHH
Confidence 5789999999999999999999999999999999999999999999999999999999999999999999999887420
Q ss_pred --------------------------------------------------------------CCC---CCc-cccccccc
Q 025655 80 --------------------------------------------------------------RPP---MAV-TNAVSWRS 93 (250)
Q Consensus 80 --------------------------------------------------------------~~~---~~~-~~~~~wR~ 93 (250)
+.+ +++ ..+.|-+.
T Consensus 147 v~~nke~ea~q~mkrKaKElqr~r~ea~rrgg~~~~~~~~~~s~g~~~~s~~~~~~~~~~~~~~~~~~sa~~~~s~pak~ 226 (512)
T KOG2635|consen 147 VMRNKEREAKQEMKRKAKELQRARKEAERRGGSLNPGFDAIGSSGYSSVSTTNAINRVESIAQKPKQQSAAKASSAPAKA 226 (512)
T ss_pred HHHhhhHHHHHHHHHHHHHHHHHHHhhhccccccCCCccccccccccCCcccchhhccccccccccccccccCCCCCchh
Confidence 000 000 00001000
Q ss_pred --cC---------------------------------------cccccceEEEEEEEeEEEEEccCCcEEEEEEEEEEEE
Q 025655 94 --EG---------------------------------------IQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKM 132 (250)
Q Consensus 94 --~~---------------------------------------~~~~~nEi~vdV~E~i~~~~~~~G~i~~~~i~G~I~~ 132 (250)
.| ..-.++-+++.+.|++++.+++||.+-+.++.|.+.+
T Consensus 227 mklG~k~~~s~~~~d~Lk~ege~ia~~~s~~g~~s~aap~~~~p~v~~e~v~i~ieEkln~~~~RDGgi~s~E~qG~lsL 306 (512)
T KOG2635|consen 227 MKLGKKTKNSDTFVDKLKGEGERIAGASSAIGSASSAAPPPTAPDVPEESVHIVIEEKLNVRLSRDGGIKSGEVQGTLSL 306 (512)
T ss_pred hhhcccccchhhHHHHhhccccccccccccccccccCCCCCCCCCCccceEEEEEeeeEeEEEcccCCccceeeeeeEEE
Confidence 00 0012334999999999999999999999999999999
Q ss_pred EEEeCCCCeEEEEeccchhhhhccCCCCCcceeccccccccccccccccCCceeEecCCCCce------EEEEEEecCC-
Q 025655 133 RTYLSGMPECKLGLNDRILLEAQGRSTKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSF------DLMTYRLNTQ- 205 (250)
Q Consensus 133 ~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~l~d~~fH~cV~~~~~~~~r~i~F~PPdg~F------~Lm~Yr~~~~- 205 (250)
+..-.--..+.|.|++.. ..+ .++++||.+|++.|.++..|...+|+..| .|++||....
T Consensus 307 rI~d~e~~~i~lkl~n~~----------~~g---~q~ktHPNlDK~~f~s~s~iglk~~~K~FPvn~~VGvLkWR~~~~d 373 (512)
T KOG2635|consen 307 RIKDEEYGDIELKLANGR----------DKG---TQLKTHPNLDKKVFLSSSLIGLKRPEKPFPVNSDVGVLKWRMVDED 373 (512)
T ss_pred EEccccccceEEEEcCCC----------Ccc---eeeeeCCCcchhhhccccccccccCCCCCCcCCcceEEEEeecccc
Confidence 998888888888887642 122 57899999999999999999999999999 8999998653
Q ss_pred --CcCcEEEEEEEEECcce---EEEEEEEEeecCCcccccceeEEeecCC
Q 025655 206 --VKPLIWVEAQVERHSRS---RVEILVKARSQFKERRCSDINGICIICT 250 (250)
Q Consensus 206 --~~P~~~v~~~~~~~~~~---~~e~~v~l~~~~~~~~~a~v~i~ip~p~ 250 (250)
..|+ .++||+++.+.. .+||++...+ ..+||.|.||+|+
T Consensus 374 es~iPl-TincWPSes~~g~dV~iEYe~~~~~-----eL~dV~i~iPlP~ 417 (512)
T KOG2635|consen 374 ESEIPL-TINCWPSESGNGYDVNIEYEAVLEC-----ELNDVIITIPLPA 417 (512)
T ss_pred cccCce-EEEeccccCCCCeEEEEEEeehhcc-----cccceEEEeeccc
Confidence 3666 679999987632 6777764344 3589999999995
No 6
>KOG2677 consensus Stoned B synaptic vesicle biogenesis protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.89 E-value=1.9e-24 Score=204.03 Aligned_cols=154 Identities=29% Similarity=0.513 Sum_probs=127.0
Q ss_pred CcccccceEEEEEEEeEEEEEccCCcEEEEEEEEEEEEEEEeCCCCeEEEEeccchhhhhc-------cCCCCCcceecc
Q 025655 95 GIQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQ-------GRSTKGKAIDLD 167 (250)
Q Consensus 95 ~~~~~~nEi~vdV~E~i~~~~~~~G~i~~~~i~G~I~~~s~LsG~P~~~l~ln~~~~~~~~-------~~~~~~~~~~l~ 167 (250)
...|..+||.|||.++.++.++++|+++...|..+|+|.|||+|.|+|.|||||..+.+.+ .+.....||+|.
T Consensus 581 k~nY~e~EI~v~~~Defsg~V~Keg~~~~~~v~tri~cL~FlsG~~ec~lgLND~~~kg~Eiv~rkDimp~~t~kwI~~~ 660 (922)
T KOG2677|consen 581 KSNYLEEEITVDVRDEFSGIVSKEGQILQHHVLTRIHCLSFLSGLAECRLGLNDILVKGNEIVLRKDIMPTTTTKWIKLH 660 (922)
T ss_pred ccccccceeEEEEEeccceeecccchhhhhhhhhhhhhhhhccCCceeEeecchhhhcccceeEeccccccccccceeee
Confidence 3479999999999999999999999999999999999999999999999999999875543 122456899999
Q ss_pred ccccccccccccccCCceeEecCCCC-ceEEEEEEecCC--CcCcEEEEEEEEECcceEEEEE--EEEeecCCc------
Q 025655 168 DIKFHQCVRLARFENDRTISFIPPDG-SFDLMTYRLNTQ--VKPLIWVEAQVERHSRSRVEIL--VKARSQFKE------ 236 (250)
Q Consensus 168 d~~fH~cV~~~~~~~~r~i~F~PPdg-~F~Lm~Yr~~~~--~~P~~~v~~~~~~~~~~~~e~~--v~l~~~~~~------ 236 (250)
+|.||.|||.+.|+++|+|.|.|||| +|+|||||+-.+ .+||.+ +..+...| .++|+. +++.+.|..
T Consensus 661 ~~~FH~cVn~~eF~~srVI~F~PlDaCrFElMRFrt~~~~~~lpftl-ks~~~V~G-a~VEvq~~~~mat~~qr~rd~~~ 738 (922)
T KOG2677|consen 661 ECRFHGCVNEDEFHNSRVILFNPLDACRFELMRFRTVFAEKTLPFTL-KSATSVNG-AEVEVQSWLRMATGFQRNRDPLT 738 (922)
T ss_pred eeeeecccchhhccccceEEecCcccceeeeeeeeeecCCCcCceee-eeeeeecc-ceeehHHHHHHHhhhhhccCccc
Confidence 99999999999999999999999999 899999999644 588864 66666554 345553 334444422
Q ss_pred -ccccceeEEeecCC
Q 025655 237 -RRCSDINGICIICT 250 (250)
Q Consensus 237 -~~~a~v~i~ip~p~ 250 (250)
..+.|+.|+.|+|.
T Consensus 739 ~vpCenI~IrfPVPs 753 (922)
T KOG2677|consen 739 QVPCENIMIRFPVPS 753 (922)
T ss_pred cCcccceeEeccCcH
Confidence 23569999999984
No 7
>PF01217 Clat_adaptor_s: Clathrin adaptor complex small chain; InterPro: IPR022775 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the small sigma and mu subunits of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and the zeta and delta subunits of various coatomer (COP) adaptors. The small sigma subunit of AP proteins have been characterised in several species [, , , ]. The sigma subunit plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The zeta subunit of coatomers (zeta-COP) is required for coatomer binding to Golgi membranes and for coat-vesicle assembly [, ]. More information about these proteins can be found at Protein of the Month: Clathrin [].; PDB: 1W63_W 2JKR_I 2VGL_S 2JKT_I 2XA7_S 2HF6_A 3TJZ_C.
Probab=99.52 E-value=2.2e-14 Score=115.71 Aligned_cols=71 Identities=34% Similarity=0.571 Sum_probs=64.7
Q ss_pred CeeecCCCCHHHHHHHHHHHHHHHHHhhcccCHHHHHhhHHHHHHHHHHHhcCCeeeecChhhhhhhhccc
Q 025655 1 MTASRQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTD 71 (250)
Q Consensus 1 v~~t~~~~n~~~~~e~L~~l~~~l~~y~g~l~e~~i~~n~~~iyelLdE~id~G~p~~t~~~~Lk~~i~~~ 71 (250)
+++++.+.|+++++++|+++.+++++|||+++|..|++||..+|++|||++|+|+|+.|+++.+.+.+.+.
T Consensus 68 ~~v~~~~eNel~~~e~l~~~v~~l~~~~~~v~e~~i~~N~~~v~~~LDEiid~G~i~etd~~~I~~~v~~~ 138 (141)
T PF01217_consen 68 VVVGDENENELLLLEFLHRLVEVLDDYFGNVSEKDILENFDLVYLILDEIIDGGIILETDPNVILKRVTMQ 138 (141)
T ss_dssp EEEESSTSBHHHHHHHHHHHHHHHHHHHSS-SHHHHHHTHHHHHHHHHHHEETTEES--THHHHHHHHHHC
T ss_pred EEEeecccchHHHHHHHHHhhhhhhhhhccccHHHHHHCHHHHHHHHHHHHhCCEEEECCHHHHHHHHHHh
Confidence 47889999999999999999999999999999999999999999999999999999999999999888664
No 8
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=98.04 E-value=5.5e-06 Score=65.79 Aligned_cols=64 Identities=27% Similarity=0.333 Sum_probs=58.8
Q ss_pred eeecCCCCHHHHHHHHHHHHHHHHHhhcccCHHHHHhhHHHHHHHHHHHhcCCeeeecChhhhh
Q 025655 2 TASRQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILS 65 (250)
Q Consensus 2 ~~t~~~~n~~~~~e~L~~l~~~l~~y~g~l~e~~i~~n~~~iyelLdE~id~G~p~~t~~~~Lk 65 (250)
++.+.+.|-+.+|+++|.|.+.+..|||+++|-.+.-||-.+|-+||||+-+|-.+.++++.+-
T Consensus 69 f~Vd~~dnEl~iL~lIh~FVE~lDr~FgnVCELdlIFNF~kv~~ILdE~i~gG~i~Es~~~~vl 132 (152)
T COG5030 69 FGVDNDDNELIILELIHNFVEILDRFFGNVCELDLIFNFQKVYAILDEMILGGEIIESSKNEVL 132 (152)
T ss_pred EEEcCCCCcchHHHHHHHHHHHHHHHhccceeeEeEeeHHHHHHHHHHHHhCCeeeecCHHHHH
Confidence 4556678999999999999999999999999999999999999999999999999999987553
No 9
>KOG0934 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.00 E-value=3.7e-06 Score=66.63 Aligned_cols=60 Identities=32% Similarity=0.407 Sum_probs=55.1
Q ss_pred eecCCCCHHHHHHHHHHHHHHHHHhhcccCHHHHHhhHHHHHHHHHHHhcCCeeeecChh
Q 025655 3 ASRQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEAN 62 (250)
Q Consensus 3 ~t~~~~n~~~~~e~L~~l~~~l~~y~g~l~e~~i~~n~~~iyelLdE~id~G~p~~t~~~ 62 (250)
....+.|-+.++|++|++.+++..|||+++|-.|.-||..+|.+|||.+-.|-.|.+..+
T Consensus 70 ~v~~~dNEL~~LE~IH~~vE~lDkYFg~VCELDiiFNfekay~ILde~~~~g~~~e~~k~ 129 (145)
T KOG0934|consen 70 GVEDNDNELAILEFIHNYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEIQETSKN 129 (145)
T ss_pred EEecCCchhhHHHHHHHHHHHHHHHhccceeeEEEEehHhHHHHHHHHhcCcchHhhhcc
Confidence 344789999999999999999999999999999999999999999999999987777655
No 10
>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.67 E-value=2.8e-05 Score=60.34 Aligned_cols=61 Identities=28% Similarity=0.337 Sum_probs=55.2
Q ss_pred cCCCCHHHHHHHHHHHHHHHHHhhcccCHHHHHhhHHHHHHHHHHHhcCCeeeecChhhhh
Q 025655 5 RQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILS 65 (250)
Q Consensus 5 ~~~~n~~~~~e~L~~l~~~l~~y~g~l~e~~i~~n~~~iyelLdE~id~G~p~~t~~~~Lk 65 (250)
....|-+..++-+|.|+++|.+|||+++|-.+.-||-.+|-++|||+=+|..|.|+...+-
T Consensus 73 d~tDnelayLe~IHlFVEvLd~fF~NVCELDlvFNFyKVy~i~DEm~l~GEi~Etsk~~vl 133 (143)
T KOG0935|consen 73 DVTDNELAYLEHIHLFVEVLDEFFHNVCELDLVFNFYKVYTIVDEMFLAGEIRETSKTKVL 133 (143)
T ss_pred ecCCchHHHHHHHHHHHHHHHHHhccccceeeeeeeeeHHHHHHHHHHhhhhhhhhHHHHH
Confidence 3456778899999999999999999999999999999999999999999999999876543
No 11
>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.19 E-value=0.00098 Score=53.91 Aligned_cols=72 Identities=18% Similarity=0.184 Sum_probs=64.3
Q ss_pred CeeecCCCCHHHHHHHHHHHHHHHHHhhcccCHHHHHhhHHHHHHHHHHHhcCCeeeecChhhhhhhhcccc
Q 025655 1 MTASRQNCNAASLLFFLHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDA 72 (250)
Q Consensus 1 v~~t~~~~n~~~~~e~L~~l~~~l~~y~g~l~e~~i~~n~~~iyelLdE~id~G~p~~t~~~~Lk~~i~~~~ 72 (250)
|.+.+...+-+-++++++-|++.|...|..++|-.+.-|+..++.+|+|++-+|....|+.+.+-.-+...+
T Consensus 74 vfvvD~sEsEL~iLDLIQvfVEtLDkCF~nVcELDliF~~~k~h~iL~EiV~GGmVlETn~neIv~av~~~n 145 (182)
T KOG0936|consen 74 VFVVDSSESELGILDLIQVFVETLDKCFENVCELDLIFNWQKVHAILAEIVMGGMVLETNMNEIVAAVDEQN 145 (182)
T ss_pred EEEEcCCcchhHHHHHHHHHHHHHHHHHHhhhhhhheeeHHHHHHHHHHHHhCCeEEeccHHHHHHHHHHhc
Confidence 356677888899999999999999999999999999999999999999999999999999987766665543
No 12
>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=96.72 E-value=0.0024 Score=52.10 Aligned_cols=70 Identities=20% Similarity=0.299 Sum_probs=60.1
Q ss_pred ecCCCCHHHHHHHHHHHHHHHHHhhcc-cCHHHHHhhHHHHHHHHHHHhcCCeeeecChhhhhhhhccccc
Q 025655 4 SRQNCNAASLLFFLHRVVDVFKHYFEE-LEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDAY 73 (250)
Q Consensus 4 t~~~~n~~~~~e~L~~l~~~l~~y~g~-l~e~~i~~n~~~iyelLdE~id~G~p~~t~~~~Lk~~i~~~~~ 73 (250)
-..+.|-++..+.|+.|.+.+.-.+.+ +....+.+|++.|.-.+||++|.|....||++++-.-+...+.
T Consensus 78 G~~~ENEl~L~svL~~l~dal~llLr~nveKr~llEN~D~i~L~~DEiiD~GvILEtdp~~ia~rv~~~~~ 148 (175)
T KOG3343|consen 78 GSEEENELMLMSVLTCLFDALSLLLRKNVEKRELLENLDLIFLALDEIIDGGVILETDPNQIAQRVALRPT 148 (175)
T ss_pred cCcchhHHHHHHHHHHHHHHHHHHHHhChhHHHHHhhhccceeehhhhccCceEEecCHHHHHHHhccCCC
Confidence 345678888999999998888887765 7777899999999999999999999999999998887776644
No 13
>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=96.07 E-value=0.46 Score=42.18 Aligned_cols=131 Identities=15% Similarity=0.164 Sum_probs=67.1
Q ss_pred EEEEEEEeEEEEEccCCcEEEEEEEEEEEEEEEeCC------CCeEEEEeccchhhhhccCCCCCcceeccccccccccc
Q 025655 103 VFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSG------MPECKLGLNDRILLEAQGRSTKGKAIDLDDIKFHQCVR 176 (250)
Q Consensus 103 i~vdV~E~i~~~~~~~G~i~~~~i~G~I~~~s~LsG------~P~~~l~ln~~~~~~~~~~~~~~~~~~l~d~~fH~cV~ 176 (250)
+...|.|.|+|.+. +|.+.++.|.|+|.+.---.- .+.+.+.|++-.. |+.+.-.+..=
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 55689999999985 578889999999988643322 3467788865432 22222211111
Q ss_pred cccccCCceeEecCCC--Cce--EEEEEEecC-----CCcCcEEEEEEEEEC-cceEEEEEEEEee-cCCc-ccccceeE
Q 025655 177 LARFENDRTISFIPPD--GSF--DLMTYRLNT-----QVKPLIWVEAQVERH-SRSRVEILVKARS-QFKE-RRCSDING 244 (250)
Q Consensus 177 ~~~~~~~r~i~F~PPd--g~F--~Lm~Yr~~~-----~~~P~~~v~~~~~~~-~~~~~e~~v~l~~-~~~~-~~~a~v~i 244 (250)
...-..+....|.++. ... ..|+|++.. ...|+++ .+.-+.. +...+-+..++.. .+.. ....|+++
T Consensus 68 ~~~~~~~~~f~~n~~~l~~~~~~~alKYqv~~~~~~~~~~Pl~l-~~~Wk~e~~~tsl~l~Y~~Np~~~~~~~~L~nv~~ 146 (257)
T PF10291_consen 68 SSSSQSDGEFWLNMSALTSHLPKQALKYQVHSDPSNLSSVPLIL-KPVWKCEPSQTSLILDYKLNPDAFASPVPLENVVF 146 (257)
T ss_dssp --EEEETTEEEE-TTTTBT-E-EEEEEEEEES--------SEEE-EEEEEE-SSEEEEEEEEEE-TTT--E-EEEEEEEE
T ss_pred ecCCCCCCcEEEehHHhhhhhhhceEEEEEeccccccCCCCeEE-EeEEEeCCceEEEEEEEEeChhhccccceeeeEEE
Confidence 0000112234443332 233 569999975 3467654 4444433 3333333333444 4443 34579999
Q ss_pred EeecC
Q 025655 245 ICIIC 249 (250)
Q Consensus 245 ~ip~p 249 (250)
.+|+.
T Consensus 147 ~v~l~ 151 (257)
T PF10291_consen 147 SVPLD 151 (257)
T ss_dssp EEEB-
T ss_pred EEEcC
Confidence 99875
No 14
>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=85.91 E-value=0.72 Score=37.75 Aligned_cols=70 Identities=14% Similarity=0.160 Sum_probs=56.2
Q ss_pred ecCCCCHHHHHHHHHHHHHHHHHhhcc-cCHHHHHhhHHHHHHHHHHHhcCCeeeecChhhhhhhhccccc
Q 025655 4 SRQNCNAASLLFFLHRVVDVFKHYFEE-LEEESLRDNFVVVYELLDEMMDFGYPQYTEANILSEFIKTDAY 73 (250)
Q Consensus 4 t~~~~n~~~~~e~L~~l~~~l~~y~g~-l~e~~i~~n~~~iyelLdE~id~G~p~~t~~~~Lk~~i~~~~~ 73 (250)
..-+.|-.+.-+.+..|...+.--+.. .++..+.+|++.+.-+.||.||.|....|+++.+.+-++.++.
T Consensus 85 ~~meeNE~~l~q~f~~ir~Al~li~k~~~dkr~v~enYDqivl~vdEtid~Gvilet~s~~ia~rv~K~p~ 155 (187)
T COG5541 85 SPMEENEPFLGQVFDEIRAALILIVKTPTDKRNVWENYDQIVLLVDETIDEGVILETKSDEIADRVPKPPN 155 (187)
T ss_pred cccccccHHHHHHHHHHHHHHHHHHcCCcchhhHHhhhceEEEeeehhcccceEeecChHHHHHhCCCCCC
Confidence 345667777777888888777766665 4555699999999999999999999999999988888776544
No 15
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=77.68 E-value=7.7 Score=32.90 Aligned_cols=66 Identities=8% Similarity=0.057 Sum_probs=55.2
Q ss_pred eeecCCCCHHHHHHHHHHHHHHHHHhhcccCH-HHHHhhHHHHHHHHHHHhcCCeeeecChhhhhhh
Q 025655 2 TASRQNCNAASLLFFLHRVVDVFKHYFEELEE-ESLRDNFVVVYELLDEMMDFGYPQYTEANILSEF 67 (250)
Q Consensus 2 ~~t~~~~n~~~~~e~L~~l~~~l~~y~g~l~e-~~i~~n~~~iyelLdE~id~G~p~~t~~~~Lk~~ 67 (250)
.|+....|.+++-.+|+.++..|.+.+..++- ..+....+.|.-+|+..++.|.-.-.+-+..|.+
T Consensus 118 LVce~hEN~lLa~~~L~~~~~~l~~~~~~l~~~~e~l~k~d~i~aiL~~fLP~GQLLFlN~~~~k~l 184 (189)
T PF15001_consen 118 LVCEPHENRLLAENTLRLFIRHLLEHLKILSQPSEVLLKSDRILAILHRFLPHGQLLFLNHRFVKQL 184 (189)
T ss_pred EEecCchhHHHHHHHHHHHHHHHHHHHHHhCcHHHhhhhHHHHHHHHHHhCCCCcEEEEcHHHHHHH
Confidence 68899999999999999999999999976544 6677789999999999999998776666555443
No 16
>KOG0647 consensus mRNA export protein (contains WD40 repeats) [RNA processing and modification]
Probab=48.05 E-value=53 Score=30.07 Aligned_cols=88 Identities=18% Similarity=0.207 Sum_probs=58.6
Q ss_pred eEEEEEccCCcEEEEEEEEEEEEEEEeCCCCeEEEEeccchhhhhccCCCCCcceeccccccccccc-cccccCCceeEe
Q 025655 110 HVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQGRSTKGKAIDLDDIKFHQCVR-LARFENDRTISF 188 (250)
Q Consensus 110 ~i~~~~~~~G~i~~~~i~G~I~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~l~d~~fH~cV~-~~~~~~~r~i~F 188 (250)
.|.+..+++|. ....|.|++-+..--.|+|.-.+.|.-+..-+ .....-.-+.++.|||--. +....++.+++|
T Consensus 203 ~va~f~d~~~~-alGsiEGrv~iq~id~~~~~~nFtFkCHR~~~----~~~~~VYaVNsi~FhP~hgtlvTaGsDGtf~F 277 (347)
T KOG0647|consen 203 CVACFQDKDGF-ALGSIEGRVAIQYIDDPNPKDNFTFKCHRSTN----SVNDDVYAVNSIAFHPVHGTLVTAGSDGTFSF 277 (347)
T ss_pred EEEEEecCCce-EeeeecceEEEEecCCCCccCceeEEEeccCC----CCCCceEEecceEeecccceEEEecCCceEEE
Confidence 56667788888 67889999999999999997777775543110 0011123467899999211 123445677777
Q ss_pred cCCCCceEEEEEEe
Q 025655 189 IPPDGSFDLMTYRL 202 (250)
Q Consensus 189 ~PPdg~F~Lm~Yr~ 202 (250)
-.-|.+-.|..|..
T Consensus 278 WDkdar~kLk~s~~ 291 (347)
T KOG0647|consen 278 WDKDARTKLKTSET 291 (347)
T ss_pred ecchhhhhhhccCc
Confidence 77777777777764
No 17
>PF09644 Mg296: Mg296 protein; InterPro: IPR019097 This protein of 129 residues is expressed in bacteria. It consists of three identical chains of five alpha helices. Two copies of each chain associate into a complex of six units of possible biological significance but of unknown function. ; PDB: 2I15_A.
Probab=34.88 E-value=67 Score=24.74 Aligned_cols=30 Identities=27% Similarity=0.441 Sum_probs=25.1
Q ss_pred HHHHHHHHHHhhcccCHHHHHhhHHHHHHH
Q 025655 17 LHRVVDVFKHYFEELEEESLRDNFVVVYEL 46 (250)
Q Consensus 17 L~~l~~~l~~y~g~l~e~~i~~n~~~iyel 46 (250)
|.++.+.++.-|..++-|+.+.||.++.|=
T Consensus 4 L~a~~~~lqt~f~~vdfEtf~~NfNl~ler 33 (121)
T PF09644_consen 4 LNAYKTFLQTEFSEVDFETFRNNFNLCLER 33 (121)
T ss_dssp HHHHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHccHHHHHHHHHHHHhc
Confidence 567888888888899999999999998764
No 18
>PRK13696 hypothetical protein; Provisional
Probab=29.41 E-value=82 Score=21.81 Aligned_cols=24 Identities=21% Similarity=0.267 Sum_probs=17.9
Q ss_pred HHHHHHHH-------HHHHHhhcccCHHHHH
Q 025655 14 LFFLHRVV-------DVFKHYFEELEEESLR 37 (250)
Q Consensus 14 ~e~L~~l~-------~~l~~y~g~l~e~~i~ 37 (250)
-+++.++. ..|.+|||.++++...
T Consensus 26 Sevi~~L~~~~~~~~~~l~~~~Gil~dee~~ 56 (62)
T PRK13696 26 SEVIRELIEKKKGNLDKLMKAFGILSEEEAE 56 (62)
T ss_pred HHHHHHHHHHhhccHHHHHHHHCCCCHHHHH
Confidence 35666776 7888999998887654
No 19
>PF13494 DUF4119: Domain of unknown function, B. Theta Gene description (DUF4119)
Probab=28.30 E-value=27 Score=25.99 Aligned_cols=36 Identities=22% Similarity=0.396 Sum_probs=29.8
Q ss_pred cccccccccc----ccccccCCceeEecCCCCceEEEEEE
Q 025655 166 LDDIKFHQCV----RLARFENDRTISFIPPDGSFDLMTYR 201 (250)
Q Consensus 166 l~d~~fH~cV----~~~~~~~~r~i~F~PPdg~F~Lm~Yr 201 (250)
.++-.||+|+ ++..+-.+..+-.+|--|.+.||.++
T Consensus 57 ~eg~~~~~~~KkL~~LA~yI~d~~ilYI~kH~GYkLMe~~ 96 (96)
T PF13494_consen 57 YEGEFHNSYSKKLKDLAEYIYDWRILYINKHGGYKLMEFS 96 (96)
T ss_pred hcccchhhHHHHHHHHHHHHhhceEEEEecCCCEEEeecC
Confidence 5778899998 45566678889999999999999864
No 20
>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=24.61 E-value=84 Score=20.17 Aligned_cols=18 Identities=39% Similarity=0.634 Sum_probs=14.2
Q ss_pred EecCCCCceEEEEEEecC
Q 025655 187 SFIPPDGSFDLMTYRLNT 204 (250)
Q Consensus 187 ~F~PPdg~F~Lm~Yr~~~ 204 (250)
.|---||.|+-|.|.-+.
T Consensus 15 vfpn~dgtftamtytksk 32 (49)
T PF07151_consen 15 VFPNQDGTFTAMTYTKSK 32 (49)
T ss_pred EeeCCCCcEEEEEEeecc
Confidence 466679999999998643
No 21
>PF02334 RTP: Replication terminator protein; InterPro: IPR003432 The bacterial replication terminator protein (RTP) plays a role in the termination of DNA replication by impeding replication fork movement. Two RTP dimers bind to the two inverted repeat regions at the termination site.; GO: 0003677 DNA binding, 0006274 DNA replication termination; PDB: 2DPU_A 2DPD_A 1F4K_A 1J0R_B 2EFW_F 2DQR_B 1BM9_B.
Probab=24.41 E-value=96 Score=24.13 Aligned_cols=32 Identities=34% Similarity=0.489 Sum_probs=20.5
Q ss_pred HHHHHhhcccCHHHHHhhHHHHHHHHHHHhcCCee
Q 025655 22 DVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYP 56 (250)
Q Consensus 22 ~~l~~y~g~l~e~~i~~n~~~iyelLdE~id~G~p 56 (250)
+.+++=|..+. -+-|-..||..|+|++|.|+-
T Consensus 39 d~lr~EFk~~G---y~P~hsEvYraLHeL~~dGil 70 (122)
T PF02334_consen 39 DELRSEFKPLG---YRPNHSEVYRALHELVDDGIL 70 (122)
T ss_dssp HHHHHHHTTTT-------HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHhhhcC---CCCCHHHHHHHHHHHHhhhHH
Confidence 34444444333 677889999999999999986
No 22
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=23.10 E-value=1.2e+02 Score=22.33 Aligned_cols=21 Identities=24% Similarity=-0.059 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHhcCCeeeecC
Q 025655 40 FVVVYELLDEMMDFGYPQYTE 60 (250)
Q Consensus 40 ~~~iyelLdE~id~G~p~~t~ 60 (250)
...|.++++++++.|+.+.|-
T Consensus 79 ~~~v~~al~~L~~eG~IYsTi 99 (102)
T PF08784_consen 79 ENEVRKALDFLSNEGHIYSTI 99 (102)
T ss_dssp HHHHHHHHHHHHHTTSEEESS
T ss_pred HHHHHHHHHHHHhCCeEeccc
Confidence 467899999999999998873
No 23
>smart00836 DALR_1 DALR anticodon binding domain. This all alpha helical domain is the anticodon binding domain of Arginyl tRNA synthetase. This domain is known as the DALR domain after characteristic conserved amino acids PUBMED:10447505.
Probab=22.17 E-value=1.6e+02 Score=22.02 Aligned_cols=45 Identities=16% Similarity=0.375 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHhhcc---cCH--HHHHhhHHHHHHHHHHHh
Q 025655 7 NCNAASLLFFLHRVVDVFKHYFEE---LEE--ESLRDNFVVVYELLDEMM 51 (250)
Q Consensus 7 ~~n~~~~~e~L~~l~~~l~~y~g~---l~e--~~i~~n~~~iyelLdE~i 51 (250)
+.+|...+++|..+...+.+||.. .++ +.++.|=..+...+..++
T Consensus 58 ~~~~~~l~~~l~~L~~~~~~fy~~v~V~~~~~~~~~~~RL~Ll~~~~~~l 107 (122)
T smart00836 58 TLEPHRLANYLYDLASAFHSFYNKCRVLGEENPELRAARLALLKAVRQVL 107 (122)
T ss_pred HCCcHHHHHHHHHHHHHHHHHHccCcccCCCCHHHHHHHHHHHHHHHHHH
Confidence 457888889999999999999975 333 457776665555544444
No 24
>PF04614 Pex19: Pex19 protein family; InterPro: IPR006708 Peroxisome(s) form an intracellular compartment, bounded by a typical lipid bilayer membrane. Peroxisome functions are often specialised by organism and cell type; two widely distributed and well-conserved functions are H2O2-based respiration and fatty acid beta-oxidation. Other functions include ether lipid (plasmalogen) synthesis and cholesterol synthesis in animals, the glyoxylate cycle in germinating seeds ("glyoxysomes"), photorespiration in leaves, glycolysis in trypanosomes ("glycosomes"), and methanol and/or amine oxidation and assimilation in some yeasts. PEX genes encode the machinery ("peroxins") required to assemble the peroxisome. Membrane assembly and maintenance requires three of these (peroxins 3, 16, and 19) and may occur without the import of the matrix (lumen) enzymes. Matrix protein import follows a branched pathway of soluble recycling receptors, with one branch for each class of peroxisome targeting sequence (two are well characterised), and a common trunk for all. At least one of these receptors, Pex5p, enters and exits peroxisomes as it functions. Proliferation of the organelle is regulated by Pex11p. Peroxisome biogenesis is remarkably conserved among eukaryotes. A group of fatal, inherited neuropathologies are recognised as peroxisome biogenesis diseases. ; GO: 0005777 peroxisome; PDB: 2WL8_B 2W85_B.
Probab=22.13 E-value=1.7e+02 Score=25.68 Aligned_cols=21 Identities=29% Similarity=0.531 Sum_probs=15.5
Q ss_pred HhhHHHHHHHHHHHhcCCeee
Q 025655 37 RDNFVVVYELLDEMMDFGYPQ 57 (250)
Q Consensus 37 ~~n~~~iyelLdE~id~G~p~ 57 (250)
..++..|.+|+++|=++|.|-
T Consensus 195 ~~~~~~i~~lmqemQ~~G~PP 215 (248)
T PF04614_consen 195 PERREKIMELMQEMQELGQPP 215 (248)
T ss_dssp HHHHHHHHHHHHHHHHT----
T ss_pred HHHHHHHHHHHHHHHHcCCCc
Confidence 788899999999999999975
No 25
>cd08339 DED_DEDD-like Death Effector Domain of DEDD and DEDD2. Death Effector Domain (DED) found in DEDD and DEDD2. Both proteins have a single N-terminal DED and a long C-terminal portion with no known domains. DEDD has been shown to block mitotic progression by inhibiting Cdk1 and to be involved in regulating the insulin signaling cascade. DEDD and DEDD2 can bind to themselves, to each other, and to the two tandem DED-containing caspases, caspase-8 and -10. In general, DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes.
Probab=21.77 E-value=1.4e+02 Score=22.26 Aligned_cols=36 Identities=25% Similarity=0.326 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhhcccCHHHHHhhHHHHHHHHHHHhcCCeeeec
Q 025655 17 LHRVVDVFKHYFEELEEESLRDNFVVVYELLDEMMDFGYPQYT 59 (250)
Q Consensus 17 L~~l~~~l~~y~g~l~e~~i~~n~~~iyelLdE~id~G~p~~t 59 (250)
||++-+++.+ .+|+..++ .+..+|+|+++++.|+..
T Consensus 5 LH~mF~iVG~---qlT~~Dv~----vLsFL~~e~~~~~~~~~~ 40 (97)
T cd08339 5 LHRMFDIVGT---HLTHRDVR----VLSFLFVDVIDDYERGMI 40 (97)
T ss_pred HHHHHHHHhh---hcchhhHH----HHHHHHHHhcccccCCCc
Confidence 5666666654 47776654 567789999998888874
No 26
>cd07956 Anticodon_Ia_Arg Anticodon-binding domain of arginyl tRNA synthetases. This domain is found in arginyl tRNA synthetases (ArgRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. ArgRS catalyzes the transfer of arginine to the 3'-end of its tRNA.
Probab=21.60 E-value=1.6e+02 Score=23.45 Aligned_cols=48 Identities=15% Similarity=0.367 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHHHHHHHhhccc----CHHHHHhhHHHHHHHHHHHhcCC
Q 025655 7 NCNAASLLFFLHRVVDVFKHYFEEL----EEESLRDNFVVVYELLDEMMDFG 54 (250)
Q Consensus 7 ~~n~~~~~e~L~~l~~~l~~y~g~l----~e~~i~~n~~~iyelLdE~id~G 54 (250)
+-+|..++.+|..+...+.+||..+ ..+.++.|=..+...+..++..|
T Consensus 93 ~~~~~~l~~~l~~L~~~~~~ffd~v~V~~~~~~i~~nRL~Ll~~v~~vl~~~ 144 (156)
T cd07956 93 TLEPHTIATYLFDLAHAFSKFYNACPVLGAEEELRNARLALVAAARQVLANG 144 (156)
T ss_pred HcCcHHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4578888899999999999999752 23467777666666665555433
Done!