Query 023277
Match_columns 284
No_of_seqs 112 out of 773
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 02:49:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023277.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023277hhsearch_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 4.7E-73 1E-77 498.7 25.9 272 9-282 160-446 (446)
2 KOG0937 Adaptor complexes medi 100.0 2.3E-65 5.1E-70 467.6 27.7 278 6-283 146-424 (424)
3 PF00928 Adap_comp_sub: Adapto 100.0 1.2E-64 2.6E-69 452.5 31.5 261 15-283 1-262 (262)
4 KOG2740 Clathrin-associated pr 100.0 3.5E-53 7.6E-58 376.1 24.8 261 3-283 154-418 (418)
5 KOG2677 Stoned B synaptic vesi 100.0 5.7E-38 1.2E-42 295.0 8.9 253 22-281 582-889 (922)
6 KOG2635 Medium subunit of clat 99.9 2.3E-24 5.1E-29 196.5 23.2 231 22-281 270-511 (512)
7 PF10291 muHD: Muniscin C-term 99.2 3.8E-08 8.3E-13 87.7 24.8 228 29-281 3-256 (257)
8 PF03504 Chlam_OMP6: Chlamydia 51.1 96 0.0021 22.7 6.8 42 166-211 44-85 (95)
9 PF07151 DUF1391: Protein of u 38.9 34 0.00074 21.7 2.3 18 113-130 15-32 (49)
10 PF08460 SH3_5: Bacterial SH3 36.0 1.5E+02 0.0032 20.5 5.7 35 239-280 27-61 (65)
11 PF11609 DUF3248: Protein of u 31.2 88 0.0019 21.3 3.5 26 197-224 5-30 (63)
12 TIGR01451 B_ant_repeat conserv 26.8 1.7E+02 0.0037 19.1 4.4 31 147-179 11-41 (53)
13 KOG0647 mRNA export protein (c 25.9 2.6E+02 0.0056 25.8 6.6 112 36-157 203-315 (347)
14 PF13598 DUF4139: Domain of un 25.7 4.9E+02 0.011 23.4 11.2 107 105-220 194-312 (317)
15 PRK09750 hypothetical protein; 24.6 62 0.0014 22.0 1.9 14 260-273 11-24 (64)
16 cd06494 p23_NUDCD2_like p23-li 23.6 94 0.002 23.1 3.0 20 166-185 14-33 (93)
17 PF10577 UPF0560: Uncharacteri 20.0 1E+03 0.022 25.0 11.7 35 10-51 62-96 (807)
No 1
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=4.7e-73 Score=498.74 Aligned_cols=272 Identities=46% Similarity=0.824 Sum_probs=251.1
Q ss_pred CCcccccccccCCCCcccceEEEEEEEeEEEEEcCCCCEEEEEEEEEEEEEEEecCCCeEEEEEccchhhhh-c------
Q 023277 9 MAVTNAVSWRSEGIQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEA-Q------ 81 (284)
Q Consensus 9 ~~~~~~~~WR~~~~~~~~neI~vdV~E~l~~~~~~~G~v~~~~V~G~v~~~s~LsG~P~~~l~ln~~~~~~~-~------ 81 (284)
...+++++||+.|++|++||+|+||+|++|.+++++|++++++|.|.|.|+++|||||+|+++|||...+++ +
T Consensus 160 sqv~G~i~WRr~Gi~ykknevfldvvErvNlLmS~~GnVLrs~VsG~V~mk~~LSGmPeckfGlNDkl~~e~kq~esks~ 239 (446)
T KOG0938|consen 160 SQVTGKIGWRREGIKYKKNEVFLDVVERVNLLMSSDGNVLRSDVSGTVDMKTHLSGMPECKFGLNDKLGMESKQSESKSD 239 (446)
T ss_pred cccccccccccccceeccceeEeEehheeeeEEcCCCCEEEeecccEEEEEEeccCCcccccccCcccceeecccccccc
Confidence 455679999999999999999999999999999999999999999999999999999999999999987652 1
Q ss_pred -cCC-----CCCceEEeccceeeeeeccccccCCceEEEeCCCCeEEEEEEEecCCCcCcEEEEEEEEEccceEEEEEEE
Q 023277 82 -GRS-----TKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLNTQVKPLIWVEAQVERHSRSRVEILVK 155 (284)
Q Consensus 82 -~~~-----~~~~~~~l~d~~fH~cV~~~~~~~~~~l~F~PPdG~F~Lm~Yr~~~~~~P~~~v~~~~~~~~~~~~e~~l~ 155 (284)
||. ++...+.|+||.||+||++++|++++.|+|+||||+|+||+||++.++..||.|.|.++..+.+++||.+.
T Consensus 240 ~~n~~~~sks~~g~v~leDc~FHqCV~L~kFn~eh~IsFvPPDGe~ELMkYr~~enInlPFrV~PiV~el~r~kie~ri~ 319 (446)
T KOG0938|consen 240 FGNKNFPSKSGKGSVLLEDCTFHQCVRLDKFNSEHIISFVPPDGEFELMKYRVTENINLPFRVTPIVTELGRTKIEYRIT 319 (446)
T ss_pred ccccCCCcccCCceEEeeccchheeeccccccccceEEEeCCCCceEeEeeeeccCcccceEeeeheecccceeEEEEEE
Confidence 111 24456899999999999999999999999999999999999999999866667889988888889999999
Q ss_pred eccCCCCcceeeeEEEEEcCCCCCCcceEEecceeEEEeCCCCEEEEEeceecCCCeeEEEEEEEecCCC-CCCCCCCCC
Q 023277 156 ARSQFKERSTATNVEIELPVSSDASNPDVRTSMGSASYVPEDEALIWKIRSFPGGKEYMLRAEFTLPSIT-AEEATPERK 234 (284)
Q Consensus 156 ~~~~~~~~~~~~~v~i~iPlP~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~~~~~~~~~l~~~~~l~~~~-~~~~~~~~~ 234 (284)
+++.|++++.+.+|.++||+|+++..+.++++.|.++|.+.+++++|+|+++.|.+|.+|++++++.+.. +...| ..
T Consensus 320 iks~f~~kl~a~~v~~rIPvP~ntv~~n~~v~~Gkaky~psen~ivWki~kf~G~tE~tlsAevels~Tt~nkq~W--tr 397 (446)
T KOG0938|consen 320 IKSLFPPKLLAKDVVVRIPVPPNTVKCNISVSNGKAKYVPSENAIVWKINKFNGLTESTLSAEVELSDTTQNKQQW--TR 397 (446)
T ss_pred EeccCCchhhhcceEEEecCCCccccceeEEecCccccCcccceEEEEecccCCcccceeEEEEEeccCccccccc--cC
Confidence 9999999999999999999999999999999999999999999999999999999999999999998765 44557 78
Q ss_pred CcEEEEEEECcccccccEEEEEEEEE-cCCCccccceEEEEEeCcEEEE
Q 023277 235 APIRVKFEIPYFTVSGIQVRYLKIIE-KSGYHALPWVRYITMAGEYELR 282 (284)
Q Consensus 235 ~pi~l~F~ip~~t~SGl~V~~l~v~~-~~~~~~~k~vrY~t~sg~Y~~R 282 (284)
+||+|+|++|+++.|||.|++++|.+ +++|+..|||||+|+||+||+|
T Consensus 398 PPIsleFeV~MFt~SGL~VrylkV~e~~Sk~~~vkWVrYitkaGsyEiR 446 (446)
T KOG0938|consen 398 PPISLEFEVPMFTNSGLVVRYLKVSEKDSKHRAVKWVRYITKAGSYEIR 446 (446)
T ss_pred CCceeEEeeeeecCCceEEEEEEEecccCCCceEEEEEEecccceeeeC
Confidence 99999999999999999999999999 5889999999999999999998
No 2
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.3e-65 Score=467.58 Aligned_cols=278 Identities=65% Similarity=1.103 Sum_probs=256.3
Q ss_pred CCCCCcccccccccCCCCcccceEEEEEEEeEEEEEcCCCCEEEEEEEEEEEEEEEecCCCeEEEEEccchhhhhccCCC
Q 023277 6 RPPMAVTNAVSWRSEGIQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQGRST 85 (284)
Q Consensus 6 ~~~~~~~~~~~WR~~~~~~~~neI~vdV~E~l~~~~~~~G~v~~~~V~G~v~~~s~LsG~P~~~l~ln~~~~~~~~~~~~ 85 (284)
+++++.+.++.||+.+++|+|||+|+||+|+++++++++|.++.++|.|+|.|||+|+|||+++|+||+..+++..+..+
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 56889999999999999999999999999999999999999999999999999999999999999999998876655333
Q ss_pred CCceEEeccceeeeeeccccccCCceEEEeCCCCeEEEEEEEecCCCcCcEEEEEEEEEccceEEEEEEEeccCCCCcce
Q 023277 86 KGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLNTQVKPLIWVEAQVERHSRSRVEILVKARSQFKERST 165 (284)
Q Consensus 86 ~~~~~~l~d~~fH~cV~~~~~~~~~~l~F~PPdG~F~Lm~Yr~~~~~~P~~~v~~~~~~~~~~~~e~~l~~~~~~~~~~~ 165 (284)
.+..+.++|++||+||++++|+++|+|+|+||||+|+||+||++....|++.+....+.++..++++.++++++|+.+..
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 44678999999999999999999999999999999999999999999999887554455677899999999999999999
Q ss_pred eeeEEEEEcCCCCCCcceEEecceeEEEeCCCCEEEEEeceecCCCeeEEEEEEEecCCCCCCCCCCCCCcEEEEEEECc
Q 023277 166 ATNVEIELPVSSDASNPDVRTSMGSASYVPEDEALIWKIRSFPGGKEYMLRAEFTLPSITAEEATPERKAPIRVKFEIPY 245 (284)
Q Consensus 166 ~~~v~i~iPlP~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~~~~~~~~~l~~~~~l~~~~~~~~~~~~~~pi~l~F~ip~ 245 (284)
+++|.|.||+|..++++.++.+.|+++|.+++++++|+|++++|+.|+++++++.+++...++.-....+||+|+|+||+
T Consensus 306 a~~v~I~iP~P~~a~~~~fk~s~G~~~~~~e~~~l~W~I~~~~gg~e~~~r~~~~lp~~~~e~~~~~~~~pi~v~FeIp~ 385 (424)
T KOG0937|consen 306 ANNVEICIPVPDDASSPSFKTSLGSAKYDPEKSALRWTIKKFVGGKEYSLRARMDLPSEEHEEQCTEGLGPIKVKFEIPY 385 (424)
T ss_pred cceEEEEeeCCCccccceEeccCCceeeecccceEEEEeccccCCceEEEEEeecCCccccCCCCcccCCceEEEEEecc
Confidence 99999999999999999999999999999999999999999999999999999999987654411127899999999999
Q ss_pred ccccccEEEEEEEEE-cCCCccccceEEEEEeCcEEEEe
Q 023277 246 FTVSGIQVRYLKIIE-KSGYHALPWVRYITMAGEYELRL 283 (284)
Q Consensus 246 ~t~SGl~V~~l~v~~-~~~~~~~k~vrY~t~sg~Y~~R~ 283 (284)
+|.||++|+++++.+ +.+|++++||||.|+||.|++|+
T Consensus 386 ~T~SgiqVrylki~ep~~~y~s~~WVRy~T~s~~Y~~r~ 424 (424)
T KOG0937|consen 386 FTVSGIQVRYLKIIEPKSQYQSLPWVRYNTQSGPYEIRV 424 (424)
T ss_pred cccCCeEEEEEEecccccCCCccceEEEEccCCceEeeC
Confidence 999999999999998 68999999999999999999994
No 3
>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=1.2e-64 Score=452.47 Aligned_cols=261 Identities=40% Similarity=0.789 Sum_probs=218.4
Q ss_pred cccccCCCCcccceEEEEEEEeEEEEEcCCCCEEEEEEEEEEEEEEEecCCCeEEEEEccchhhhhccCCCCCceEEecc
Q 023277 15 VSWRSEGIQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQGRSTKGKAIDLDD 94 (284)
Q Consensus 15 ~~WR~~~~~~~~neI~vdV~E~l~~~~~~~G~v~~~~V~G~v~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~l~d 94 (284)
+|||+.+++|++|||||||.|+|+++++++|.++.++|.|+|.|+++|+|+|+|+|.||++... ..+++.++|
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 6999999999999999999999999999999999999999999999999999999999988432 124567999
Q ss_pred ceeeeeeccccccCCceEEEeCCCCeEEEEEEEecCCCcCcEEEEEEEEEccceEEEEEEEeccCCCCcceeeeEEEEEc
Q 023277 95 IKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLNTQVKPLIWVEAQVERHSRSRVEILVKARSQFKERSTATNVEIELP 174 (284)
Q Consensus 95 ~~fH~cV~~~~~~~~~~l~F~PPdG~F~Lm~Yr~~~~~~P~~~v~~~~~~~~~~~~e~~l~~~~~~~~~~~~~~v~i~iP 174 (284)
++||||||+++|++++.|+|+||||+|+||+||++....+|+.+.|++...+++++++.++++++++....+++|.|+||
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 99999999999999999999999999999999998888778888998888667799999999999988788999999999
Q ss_pred CCCCCCcceEEecceeEEEeCCCCEEEEEeceecCCCeeEEEEEEEecCCCCCCCCCCCCCcEEEEEEECcccccccEEE
Q 023277 175 VSSDASNPDVRTSMGSASYVPEDEALIWKIRSFPGGKEYMLRAEFTLPSITAEEATPERKAPIRVKFEIPYFTVSGIQVR 254 (284)
Q Consensus 175 lP~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~~~~~~~~~l~~~~~l~~~~~~~~~~~~~~pi~l~F~ip~~t~SGl~V~ 254 (284)
+|.++..+.+..+.|+++|+..+++++|+|++++++.++.++|++++......+.+ ..++||+|+|++|++++||++|+
T Consensus 154 lP~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~~~~~~~~~l~~~l~~~~~~~~~~~-~~~~pi~v~F~~~~~~~Sgl~V~ 232 (262)
T PF00928_consen 154 LPPGTSSPSIESSDGSAEYDEEENALVWKIKKLPGGSESTLSGTLEFSSPSSVPSD-WSFFPISVEFTIPGYTLSGLKVR 232 (262)
T ss_dssp --TTEEEEEEEESSSEEEEETGCTEEEEEEEEEETSEEEEEEEEEEEEEECCSS-S------EEEEEEESTSETTT-EEE
T ss_pred cCCccccceeeecCceEEEEccCCEEEEEECCccCcccccEEEEEEecCCCccccc-ccceeEEEEEEeCCcccCCCEEE
Confidence 99998899999999999999999999999999999999999999999875544332 26899999999999999999999
Q ss_pred EEEEEEc-CCCccccceEEEEEeCcEEEEe
Q 023277 255 YLKIIEK-SGYHALPWVRYITMAGEYELRL 283 (284)
Q Consensus 255 ~l~v~~~-~~~~~~k~vrY~t~sg~Y~~R~ 283 (284)
++++.+. .+|+|+|||||.|+||+|++|+
T Consensus 233 ~l~v~~~~~~~~~~k~vky~t~s~~Y~iR~ 262 (262)
T PF00928_consen 233 SLDVVNEDENYKPYKWVKYVTKSGSYEIRT 262 (262)
T ss_dssp EEEEE-SSCGGGSEEEEEEEEEEEEEEE--
T ss_pred EEEeEecCCCCCCcccEEEEEEcCcEEEcC
Confidence 9999883 6889999999999999999995
No 4
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=3.5e-53 Score=376.12 Aligned_cols=261 Identities=27% Similarity=0.544 Sum_probs=229.4
Q ss_pred ccCCCCCCcccccccccCCCCcccceEEEEEEEeEEEEEcCCCCEEEEEEEEEEEEEEEecCCCeEEEEEccchhhhhcc
Q 023277 3 VTQRPPMAVTNAVSWRSEGIQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQG 82 (284)
Q Consensus 3 ~~~~~~~~~~~~~~WR~~~~~~~~neI~vdV~E~l~~~~~~~G~v~~~~V~G~v~~~s~LsG~P~~~l~ln~~~~~~~~~ 82 (284)
+++.+|++..+.+|||+.+.+|++||.||||+|+++|+++++|.+..++|.|.|.|+|+|+|||++.|.|+++.
T Consensus 154 ~~~~lPtg~~s~VPWR~~~~Ky~nNE~yvdvlEeidai~~k~gslv~~eI~g~vd~~~qLsgmPdltlsl~np~------ 227 (418)
T KOG2740|consen 154 VSDTLPTGALSNVPWRTAGVKYTNNEAYVDVLEEIDAIVDKKGSLVFGEIQGIVDVCSQLSGMPDLTLSLNNPR------ 227 (418)
T ss_pred ccccCCCcccccccccccCcccccchhhhhhhheeheEecCCCCEEEEEEEEEEEEEEeecCCCceEEEccCcc------
Confidence 67789999999999999999999999999999999999999999999999999999999999999999999874
Q ss_pred CCCCCceEEeccceeeeeeccccccCCceEEEeCCCCeEEEEEEEecCC--CcCcEEEEEEEEEccce--EEEEEEEecc
Q 023277 83 RSTKGKAIDLDDIKFHQCVRLARFENDRTISFIPPDGSFDLMTYRLNTQ--VKPLIWVEAQVERHSRS--RVEILVKARS 158 (284)
Q Consensus 83 ~~~~~~~~~l~d~~fH~cV~~~~~~~~~~l~F~PPdG~F~Lm~Yr~~~~--~~P~~~v~~~~~~~~~~--~~e~~l~~~~ 158 (284)
.|+|++|||||+..+|++++.|+|+||||+|.||+||++.+ ...|+.+.++....+.. ++++.+..+.
T Consensus 228 --------~L~dvsfHpcVr~krwe~~~~lsFIPPDGkFrLlsy~v~~~~~v~~pvyv~~~i~l~~~~~~ri~~tvg~~~ 299 (418)
T KOG2740|consen 228 --------LLGDVSFHPCVRYKRWESHSVLSFIPPDGKFRLLSYRVDAQNQVAIPVYVKNSISLDSNHQGRISLTVGPKK 299 (418)
T ss_pred --------ccCCcccccceeecccccccceEEcCCCCcEEEEEEEEehhhccccceEEeeeeccCCCceEEEEEeccccc
Confidence 38999999999999999999999999999999999999865 35566777776665433 4555554444
Q ss_pred CCCCcceeeeEEEEEcCCCCCCcceEEecceeEEEeCCCCEEEEEeceecCCCeeEEEEEEEecCCCCCCCCCCCCCcEE
Q 023277 159 QFKERSTATNVEIELPVSSDASNPDVRTSMGSASYVPEDEALIWKIRSFPGGKEYMLRAEFTLPSITAEEATPERKAPIR 238 (284)
Q Consensus 159 ~~~~~~~~~~v~i~iPlP~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~~~~~~~~~l~~~~~l~~~~~~~~~~~~~~pi~ 238 (284)
..++ ..+.+.|.+..|+.........++|+..++...+.+-|+++++..+.-+.|+|++.+....... . .++.++
T Consensus 300 ~~gK--~ie~itVt~~~pn~i~~~~k~~~~g~~~~~~~~k~l~W~~~~i~tg~lp~Lkg~~~~e~~~sk~-~--~l~t~~ 374 (418)
T KOG2740|consen 300 KMGK--TIELITVTVQDPNEIAYASKILTHGTFTNSIIMKQLTWTFGSIATGKLPVLKGTINLEPGFSKK-V--DLPTLS 374 (418)
T ss_pred cccc--eeEeEEEEecCccceeeeecccccceeEeecccceeEEEeecccCCcccccccccccCCCCCcc-c--cCcccc
Confidence 4433 4577889999999988888888999999999999999999999999989999999887543222 2 688999
Q ss_pred EEEEECcccccccEEEEEEEEEcCCCccccceEEEEEeCcEEEEe
Q 023277 239 VKFEIPYFTVSGIQVRYLKIIEKSGYHALPWVRYITMAGEYELRL 283 (284)
Q Consensus 239 l~F~ip~~t~SGl~V~~l~v~~~~~~~~~k~vrY~t~sg~Y~~R~ 283 (284)
|+|++.+.++||++|+.|++.+. .|++|||+||.|+||.+++|+
T Consensus 375 Lqykiqg~alsglkVe~Ldm~~~-~~k~yKGvKy~t~agnfqvR~ 418 (418)
T KOG2740|consen 375 LQYKIQGQALSGLKVERLDMYGE-PYKPYKGVKYKTKAGNFQVRL 418 (418)
T ss_pred eeeeeeeeeccceEEEeeeecCC-CCccccceEEEEeeeeEEEeC
Confidence 99999999999999999999874 678999999999999999996
No 5
>KOG2677 consensus Stoned B synaptic vesicle biogenesis protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=5.7e-38 Score=294.95 Aligned_cols=253 Identities=27% Similarity=0.480 Sum_probs=209.8
Q ss_pred CCcccceEEEEEEEeEEEEEcCCCCEEEEEEEEEEEEEEEecCCCeEEEEEccchhhhhc---cCC----CCCceEEecc
Q 023277 22 IQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQ---GRS----TKGKAIDLDD 94 (284)
Q Consensus 22 ~~~~~neI~vdV~E~l~~~~~~~G~v~~~~V~G~v~~~s~LsG~P~~~l~ln~~~~~~~~---~~~----~~~~~~~l~d 94 (284)
..|..+||.|||.++.+++++++|.++...|.-+|.|.|||+|+++|+|+|||....+.. .++ ....|++|.+
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 468999999999999999999999999999999999999999999999999998764322 111 3668999999
Q ss_pred ceeeeeeccccccCCceEEEeCCCC-eEEEEEEEecCC--CcCcEEEEEEEEEccceEEEEEEEe--ccC------CCCc
Q 023277 95 IKFHQCVRLARFENDRTISFIPPDG-SFDLMTYRLNTQ--VKPLIWVEAQVERHSRSRVEILVKA--RSQ------FKER 163 (284)
Q Consensus 95 ~~fH~cV~~~~~~~~~~l~F~PPdG-~F~Lm~Yr~~~~--~~P~~~v~~~~~~~~~~~~e~~l~~--~~~------~~~~ 163 (284)
|.||-||+.+.|+++|+|.|.|+|| .|+|||||+-.+ .+|+ .+...+.- ++.++|+..-+ .+. -...
T Consensus 662 ~~FH~cVn~~eF~~srVI~F~PlDaCrFElMRFrt~~~~~~lpf-tlks~~~V-~Ga~VEvq~~~~mat~~qr~rd~~~~ 739 (922)
T KOG2677|consen 662 CRFHGCVNEDEFHNSRVILFNPLDACRFELMRFRTVFAEKTLPF-TLKSATSV-NGAEVEVQSWLRMATGFQRNRDPLTQ 739 (922)
T ss_pred eeeecccchhhccccceEEecCcccceeeeeeeeeecCCCcCce-eeeeeeee-ccceeehHHHHHHHhhhhhccCcccc
Confidence 9999999999999999999999999 889999999654 3555 55443333 34567665322 222 2334
Q ss_pred ceeeeEEEEEcCCCCC--------------------------------CcceEEecceeEEEeCCCCEEEEEeceecCC-
Q 023277 164 STATNVEIELPVSSDA--------------------------------SNPDVRTSMGSASYVPEDEALIWKIRSFPGG- 210 (284)
Q Consensus 164 ~~~~~v~i~iPlP~~~--------------------------------~~~~~~~~~G~~~~~~~~~~l~W~I~~~~~~- 210 (284)
+.|+||.|++|+|..+ +.+.++++.|+++|++..+.|+|+|++++..
T Consensus 740 vpCenI~IrfPVPs~WIk~fr~e~~~g~kSlkaK~nR~a~~gsl~~~~sepvi~vt~G~AKYEhay~siVWrI~RLPdKn 819 (922)
T KOG2677|consen 740 VPCENIMIRFPVPSEWIKNFRRESVLGEKSLKAKVNRGASFGSLSVSGSEPVIRVTLGTAKYEHAYNSIVWRINRLPDKN 819 (922)
T ss_pred CcccceeEeccCcHHHHHHHHHHhhhccchhhhhhcccccccchhhccCCceEEEeecchhhHHhhhhheeecccCCccc
Confidence 6799999999999843 3467899999999999999999999998864
Q ss_pred ----CeeEEEEEEEecCCCCCCCCCCCCCcEEEEEEECcccccccEEEEEEEEEcCCCccccceEEEEEeCcEEE
Q 023277 211 ----KEYMLRAEFTLPSITAEEATPERKAPIRVKFEIPYFTVSGIQVRYLKIIEKSGYHALPWVRYITMAGEYEL 281 (284)
Q Consensus 211 ----~~~~l~~~~~l~~~~~~~~~~~~~~pi~l~F~ip~~t~SGl~V~~l~v~~~~~~~~~k~vrY~t~sg~Y~~ 281 (284)
.++.|.|.++|.+++..+++ -.+.+.|+|.+|..++|...|++|.|.. ...+.|||+|... .+|++
T Consensus 820 sa~~hpHcl~c~lELgSd~evPs~--f~p~~~V~FsmP~t~aS~t~VRSisVE~--~~~v~K~V~y~A~-Y~yqv 889 (922)
T KOG2677|consen 820 SASGHPHCLFCHLELGSDREVPSR--FAPHVNVEFSMPTTSASKTSVRSISVED--KTDVRKWVNYSAH-YSYQV 889 (922)
T ss_pred cccCCCeeEEEEEeccccccCchh--hccccceeeeccccccccceeeeeeccc--cccHHHHHhhhhh-eeeee
Confidence 36899999999998877766 6778999999999999999999999976 4459999999664 55654
No 6
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.93 E-value=2.3e-24 Score=196.50 Aligned_cols=231 Identities=16% Similarity=0.240 Sum_probs=180.9
Q ss_pred CCcccceEEEEEEEeEEEEEcCCCCEEEEEEEEEEEEEEEecCCCeEEEEEccchhhhhccCCCCCceEEeccceeeeee
Q 023277 22 IQYKKNEVFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQGRSTKGKAIDLDDIKFHQCV 101 (284)
Q Consensus 22 ~~~~~neI~vdV~E~l~~~~~~~G~v~~~~V~G~v~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~l~d~~fH~cV 101 (284)
....+|.||+.+.|+|++.+++||.+.+.++.|.+.++........+.|.|++... . -.++++||.+
T Consensus 270 p~v~~e~v~i~ieEkln~~~~RDGgi~s~E~qG~lsLrI~d~e~~~i~lkl~n~~~----------~---g~q~ktHPNl 336 (512)
T KOG2635|consen 270 PDVPEESVHIVIEEKLNVRLSRDGGIKSGEVQGTLSLRIKDEEYGDIELKLANGRD----------K---GTQLKTHPNL 336 (512)
T ss_pred CCCccceEEEEEeeeEeEEEcccCCccceeeeeeEEEEEccccccceEEEEcCCCC----------c---ceeeeeCCCc
Confidence 33456779999999999999999999999999999999999999999999986431 1 2578999999
Q ss_pred ccccccCCceEEEeCCCCeEE------EEEEEecCC--CcCcEEEEEEEEEccc-e--EEEEEEEeccCCCCcceeeeEE
Q 023277 102 RLARFENDRTISFIPPDGSFD------LMTYRLNTQ--VKPLIWVEAQVERHSR-S--RVEILVKARSQFKERSTATNVE 170 (284)
Q Consensus 102 ~~~~~~~~~~l~F~PPdG~F~------Lm~Yr~~~~--~~P~~~v~~~~~~~~~-~--~~e~~l~~~~~~~~~~~~~~v~ 170 (284)
|++.|.++..|.+++|+..|+ ||+||.... ..-|++++||+.+.+. . .+||++...+ .++||.
T Consensus 337 DK~~f~s~s~iglk~~~K~FPvn~~VGvLkWR~~~~des~iPlTincWPSes~~g~dV~iEYe~~~~~------eL~dV~ 410 (512)
T KOG2635|consen 337 DKKVFLSSSLIGLKRPEKPFPVNSDVGVLKWRMVDEDESEIPLTINCWPSESGNGYDVNIEYEAVLEC------ELNDVI 410 (512)
T ss_pred chhhhccccccccccCCCCCCcCCcceEEEEeecccccccCceEEEeccccCCCCeEEEEEEeehhcc------cccceE
Confidence 999999999999999999995 899999653 3555688999887553 3 5677763333 467999
Q ss_pred EEEcCCCCCCcceEEecceeEEEeCCCCEEEEEeceecCCCeeEEEEEEEecCCCCCCCCCCCCCcEEEEEEECcccccc
Q 023277 171 IELPVSSDASNPDVRTSMGSASYVPEDEALIWKIRSFPGGKEYMLRAEFTLPSITAEEATPERKAPIRVKFEIPYFTVSG 250 (284)
Q Consensus 171 i~iPlP~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~~~~~~~~~l~~~~~l~~~~~~~~~~~~~~pi~l~F~ip~~t~SG 250 (284)
|.||+|.+. .|++.+.+|.+.|+..++.+.|.|+.+.. + .+|.++|.-.. .+.+ .++|++|+|... .+++|
T Consensus 411 i~iPlP~~i-apsv~~~Dge~~~~~~~~~leW~I~~Ia~-N---~SGslEFs~~~-~~~~--~fFPl~VsF~s~-~~ftg 481 (512)
T KOG2635|consen 411 ITIPLPANI-APSVGECDGEYRYDERKNVLEWSIGVIAK-N---FSGSLEFSCPA-SDPD--GFFPLSVSFTSD-TVFTG 481 (512)
T ss_pred EEeeccccc-CCccceecceEEeccccceeEEEeeeecc-C---CCCcEEEeecC-CCCC--ceeeEEEEEEec-ccccc
Confidence 999999988 89999999999999999999999999933 3 35556664221 2334 799999999988 79999
Q ss_pred cEEEEEEEEEcCCCccccceEEEEEeCcEEE
Q 023277 251 IQVRYLKIIEKSGYHALPWVRYITMAGEYEL 281 (284)
Q Consensus 251 l~V~~l~v~~~~~~~~~k~vrY~t~sg~Y~~ 281 (284)
+.|..+.-... ...+.--++-.-.+..|++
T Consensus 482 l~vqkVv~~~~-~~~~~y~~~t~f~~dky~V 511 (512)
T KOG2635|consen 482 LFVQKVVRNDG-HAPVRYSVETTFEVDKYEV 511 (512)
T ss_pred eEEEEEEEcCC-CCCceeEEEEEEEeeeeEe
Confidence 99998876442 1112222333333567765
No 7
>PF10291 muHD: Muniscin C-terminal mu homology domain; InterPro: IPR018808 The muniscins are a family of endocytic adaptors that is conserved from yeast to humans.This C-terminal domain is structurally similar to mu homology domains, and is the region of the muniscin proteins involved in the interactions with the endocytic adaptor-scaffold proteins Ede1-eps15. This interaction influences muniscin localisation. The muniscins provide a combined adaptor-membrane-tubulation activity that is important for regulating endocytosis.; PDB: 3G9H_A.
Probab=99.16 E-value=3.8e-08 Score=87.73 Aligned_cols=228 Identities=17% Similarity=0.266 Sum_probs=118.5
Q ss_pred EEEEEEEeEEEEEcCCCCEEEEEEEEEEEEEEEecC------CCeEEEEEccchhhhhccCCCCCceEEeccceeeeeec
Q 023277 29 VFLDVVEHVNILVNSNGQIIRSDVVGALKMRTYLSG------MPECKLGLNDRILLEAQGRSTKGKAIDLDDIKFHQCVR 102 (284)
Q Consensus 29 I~vdV~E~l~~~~~~~G~v~~~~V~G~v~~~s~LsG------~P~~~l~ln~~~~~~~~~~~~~~~~~~l~d~~fH~cV~ 102 (284)
+-..|.|.+||.+.. |.+.+..|.|+|.+.---.- .+.+.+.|++...+ +.+.-.+..=
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 567899999999976 78999999999998543222 34567777655432 2222211111
Q ss_pred cccccCCceEEEeCCC--CeE--EEEEEEecCC----CcCcEEEEEEEEEcc-ceEEEEEEEecc-CCCCcceeeeEEEE
Q 023277 103 LARFENDRTISFIPPD--GSF--DLMTYRLNTQ----VKPLIWVEAQVERHS-RSRVEILVKARS-QFKERSTATNVEIE 172 (284)
Q Consensus 103 ~~~~~~~~~l~F~PPd--G~F--~Lm~Yr~~~~----~~P~~~v~~~~~~~~-~~~~e~~l~~~~-~~~~~~~~~~v~i~ 172 (284)
...-.++....|.++. ... ..|+|++... ..+|+.+.+..+-.. ...+-+..++.+ .+.....++||.|.
T Consensus 68 ~~~~~~~~~f~~n~~~l~~~~~~~alKYqv~~~~~~~~~~Pl~l~~~Wk~e~~~tsl~l~Y~~Np~~~~~~~~L~nv~~~ 147 (257)
T PF10291_consen 68 SSSSQSDGEFWLNMSALTSHLPKQALKYQVHSDPSNLSSVPLILKPVWKCEPSQTSLILDYKLNPDAFASPVPLENVVFS 147 (257)
T ss_dssp --EEEETTEEEE-TTTTBT-E-EEEEEEEEES--------SEEEEEEEEE-SSEEEEEEEEEE-TTT--E-EEEEEEEEE
T ss_pred ecCCCCCCcEEEehHHhhhhhhhceEEEEEeccccccCCCCeEEEeEEEeCCceEEEEEEEEeChhhccccceeeeEEEE
Confidence 0011122234444332 222 4699999762 344555555444332 234444444444 44445678999999
Q ss_pred EcCCCC-CCcceEEecceeEEEeCCCCEEEEEeceec--CCCe-eEEEEEEEecCCCCCCCCCCCCCcEEEEEEEC-ccc
Q 023277 173 LPVSSD-ASNPDVRTSMGSASYVPEDEALIWKIRSFP--GGKE-YMLRAEFTLPSITAEEATPERKAPIRVKFEIP-YFT 247 (284)
Q Consensus 173 iPlP~~-~~~~~~~~~~G~~~~~~~~~~l~W~I~~~~--~~~~-~~l~~~~~l~~~~~~~~~~~~~~pi~l~F~ip-~~t 247 (284)
+++... +.++.... .+.|..+++.|.|+|+.+. ++.+ ..|.|+|...... . .-.+|.++|++. +-+
T Consensus 148 v~l~g~~~ts~~skP---~g~~~~e~~ri~Wrl~el~~~~~~~~~kL~ARf~~~~~~----~--~p~~v~vkF~~~~~~~ 218 (257)
T PF10291_consen 148 VPLDGGRATSAQSKP---QGTWNKEKNRITWRLPELSLTSEGEGGKLIARFMTSGGP----S--RPGGVEVKFEIEGGST 218 (257)
T ss_dssp EEB-SS-EEEEEESS---S--B-SSS-EEEEE-SSEEEETT---EEEEEEEEESS----------SS-EEEEEEE---S-
T ss_pred EEcCCccccccccCC---CccccCCCcEEEEECCcccccCCCCCceEEEEEECCCCC----C--CCceEEEEEEEcCCCc
Confidence 999876 33333333 3567799999999998755 3333 6899998766532 1 467899999999 888
Q ss_pred ccccEEEEEEEEEcC-----CCccccceEEEEEeCcEEE
Q 023277 248 VSGIQVRYLKIIEKS-----GYHALPWVRYITMAGEYEL 281 (284)
Q Consensus 248 ~SGl~V~~l~v~~~~-----~~~~~k~vrY~t~sg~Y~~ 281 (284)
.||+.|.-+.-.+.. +|+.. -++-...||.|..
T Consensus 219 ~sg~~i~~~~~~~~~dp~~~~w~~~-~~~r~~~sGkY~~ 256 (257)
T PF10291_consen 219 LSGLGISLVYQDDEEDPPGGGWRLV-LVKRKLVSGKYIA 256 (257)
T ss_dssp SS----EEEEEESSS-TT----EE--EEEEEEEEEEEE-
T ss_pred ccCcEEEEeecccccCCCCCcceEE-EEEEEEeeeEEec
Confidence 999998877222111 22222 4555566899973
No 8
>PF03504 Chlam_OMP6: Chlamydia cysteine-rich outer membrane protein 6; InterPro: IPR003506 Three cysteine-rich proteins (also believed to be lipoproteins) make up the extracellular matrix of the Chlamydial outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. As these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism. The largest of these is the major outer membrane protein (MOMP), and constitutes around 60% of the total protein for the membrane []. OMP6 is the second largest, with a molecular mass of 58kDa, while the OMP3 protein is ~15kDa []. MOMP is believed to elicit the strongest immune response, and has recently been linked to heart disease through its sequence similarity to a murine heart-muscle specific alpha myosin []. The OMP6 family plays a structural role in the outer membrane during the EB stage of the Chlamydial cell, and different biovars show a small, yet highly significant, change at peptide charge level []. Members of this family include Chlamydia trachomatis, Chlamydia pneumoniae and Chlamydia psittaci.; GO: 0005201 extracellular matrix structural constituent
Probab=51.07 E-value=96 Score=22.73 Aligned_cols=42 Identities=24% Similarity=0.373 Sum_probs=26.7
Q ss_pred eeeEEEEEcCCCCCCcceEEecceeEEEeCCCCEEEEEeceecCCC
Q 023277 166 ATNVEIELPVSSDASNPDVRTSMGSASYVPEDEALIWKIRSFPGGK 211 (284)
Q Consensus 166 ~~~v~i~iPlP~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~~~~~~ 211 (284)
+-||.|.-.||-+.+ +-.++-.++ -...+.|+|+|+++..+.
T Consensus 44 cvnVviTqqLPce~e---FV~SdPett-p~~D~kLVW~Ig~l~~G~ 85 (95)
T PF03504_consen 44 CVNVVITQQLPCEVE---FVRSDPETT-PTPDGKLVWKIGRLGQGE 85 (95)
T ss_pred eeEEEEeecCCcceE---EEecCCccc-cCCCCEEEEEeccccCCc
Confidence 558899999998643 222221111 124578999999987665
No 9
>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=38.89 E-value=34 Score=21.72 Aligned_cols=18 Identities=39% Similarity=0.634 Sum_probs=14.6
Q ss_pred EEeCCCCeEEEEEEEecC
Q 023277 113 SFIPPDGSFDLMTYRLNT 130 (284)
Q Consensus 113 ~F~PPdG~F~Lm~Yr~~~ 130 (284)
.|---||.|+.|.|.-+.
T Consensus 15 vfpn~dgtftamtytksk 32 (49)
T PF07151_consen 15 VFPNQDGTFTAMTYTKSK 32 (49)
T ss_pred EeeCCCCcEEEEEEeecc
Confidence 477789999999998543
No 10
>PF08460 SH3_5: Bacterial SH3 domain; InterPro: IPR013667 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The SH3 domain has been found in a number of different bacterial proteins including glycyl-glycine endopeptidase, bacteriocin and some hypothetical proteins.; GO: 0016787 hydrolase activity; PDB: 1R77_B.
Probab=36.03 E-value=1.5e+02 Score=20.49 Aligned_cols=35 Identities=31% Similarity=0.655 Sum_probs=21.5
Q ss_pred EEEEECcccccccEEEEEEEEEcCCCccccceEEEEEeCcEE
Q 023277 239 VKFEIPYFTVSGIQVRYLKIIEKSGYHALPWVRYITMAGEYE 280 (284)
Q Consensus 239 l~F~ip~~t~SGl~V~~l~v~~~~~~~~~k~vrY~t~sg~Y~ 280 (284)
+-+..+ -|-.|.+-.+....+ +.|++|...+|.+-
T Consensus 27 ~~~~~~----~G~~V~YD~~~~~dG---y~Wisy~~~sG~r~ 61 (65)
T PF08460_consen 27 VVGTYP----KGQSVNYDQVIKADG---YVWISYISYSGQRR 61 (65)
T ss_dssp EEEEE-----TT-EEEEEEEEEETT---EEEEEEE-TT--EE
T ss_pred eEEEEC----CCCEEEEEEEEEeCC---EEEEEEECCCCeEE
Confidence 445555 677888877766554 78999998888543
No 11
>PF11609 DUF3248: Protein of unknown function (DUF3248); InterPro: IPR021650 This family of proteins is thought to be the product of the gene TT1592 from Thermus thermophilus however this cannot be confirmed. Currently there is no known function. ; PDB: 2E6X_A.
Probab=31.19 E-value=88 Score=21.35 Aligned_cols=26 Identities=19% Similarity=0.377 Sum_probs=16.2
Q ss_pred CCEEEEEeceecCCCeeEEEEEEEecCC
Q 023277 197 DEALIWKIRSFPGGKEYMLRAEFTLPSI 224 (284)
Q Consensus 197 ~~~l~W~I~~~~~~~~~~l~~~~~l~~~ 224 (284)
.+.++|+|++-..+.. +-..+.+.+.
T Consensus 5 g~~LvWRiGk~e~e~~--vvVRvG~Asa 30 (63)
T PF11609_consen 5 GQHLVWRIGKAEAEEV--VVVRVGLASA 30 (63)
T ss_dssp T--EEEEEEE-TTSSS--EEEEEEEGGG
T ss_pred cceeEEEeccccccCe--EEEEEecccc
Confidence 4679999999776665 4555667653
No 12
>TIGR01451 B_ant_repeat conserved repeat domain. This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins.
Probab=26.84 E-value=1.7e+02 Score=19.05 Aligned_cols=31 Identities=16% Similarity=0.125 Sum_probs=23.0
Q ss_pred ceEEEEEEEeccCCCCcceeeeEEEEEcCCCCC
Q 023277 147 RSRVEILVKARSQFKERSTATNVEIELPVSSDA 179 (284)
Q Consensus 147 ~~~~e~~l~~~~~~~~~~~~~~v~i~iPlP~~~ 179 (284)
+..++|+|.++..-. ..+++|.|.=+||.+.
T Consensus 11 Gd~v~Yti~v~N~g~--~~a~~v~v~D~lP~g~ 41 (53)
T TIGR01451 11 GDTITYTITVTNNGN--VPATNVVVTDILPSGT 41 (53)
T ss_pred CCEEEEEEEEEECCC--CceEeEEEEEcCCCCC
Confidence 447888888874433 2478999999999864
No 13
>KOG0647 consensus mRNA export protein (contains WD40 repeats) [RNA processing and modification]
Probab=25.86 E-value=2.6e+02 Score=25.78 Aligned_cols=112 Identities=17% Similarity=0.164 Sum_probs=67.5
Q ss_pred eEEEEEcCCCCEEEEEEEEEEEEEEEecCCCeEEEEEccchhhhhccCCCCCceEEeccceeeeeec-cccccCCceEEE
Q 023277 36 HVNILVNSNGQIIRSDVVGALKMRTYLSGMPECKLGLNDRILLEAQGRSTKGKAIDLDDIKFHQCVR-LARFENDRTISF 114 (284)
Q Consensus 36 ~l~~~~~~~G~v~~~~V~G~v~~~s~LsG~P~~~l~ln~~~~~~~~~~~~~~~~~~l~d~~fH~cV~-~~~~~~~~~l~F 114 (284)
.|.+..|++|. ....|.|.+.++.-..++|.-.+.|......+. . ..+-.-+-++.|||--. +..-.+|..++|
T Consensus 203 ~va~f~d~~~~-alGsiEGrv~iq~id~~~~~~nFtFkCHR~~~~-~---~~~VYaVNsi~FhP~hgtlvTaGsDGtf~F 277 (347)
T KOG0647|consen 203 CVACFQDKDGF-ALGSIEGRVAIQYIDDPNPKDNFTFKCHRSTNS-V---NDDVYAVNSIAFHPVHGTLVTAGSDGTFSF 277 (347)
T ss_pred EEEEEecCCce-EeeeecceEEEEecCCCCccCceeEEEeccCCC-C---CCceEEecceEeecccceEEEecCCceEEE
Confidence 46667788887 566799999999999999977777755431110 0 01122356789999221 122235777777
Q ss_pred eCCCCeEEEEEEEecCCCcCcEEEEEEEEEccceEEEEEEEec
Q 023277 115 IPPDGSFDLMTYRLNTQVKPLIWVEAQVERHSRSRVEILVKAR 157 (284)
Q Consensus 115 ~PPdG~F~Lm~Yr~~~~~~P~~~v~~~~~~~~~~~~e~~l~~~ 157 (284)
=.-|.+-.|..|..-.+ |+.. |.+.. ++.-|-|-+.-.
T Consensus 278 WDkdar~kLk~s~~~~q---pItc-c~fn~-~G~ifaYA~gYD 315 (347)
T KOG0647|consen 278 WDKDARTKLKTSETHPQ---PITC-CSFNR-NGSIFAYALGYD 315 (347)
T ss_pred ecchhhhhhhccCcCCC---ccce-eEecC-CCCEEEEEeecc
Confidence 77777777777653322 4332 44443 334566666543
No 14
>PF13598 DUF4139: Domain of unknown function (DUF4139)
Probab=25.69 E-value=4.9e+02 Score=23.36 Aligned_cols=107 Identities=19% Similarity=0.321 Sum_probs=56.4
Q ss_pred cccCCceEEEeCCCCeEEEEEEEecCCCcCcEEEEEEEE---E----cc---ceEEEEEEEeccCCCCcceeeeEEEEEc
Q 023277 105 RFENDRTISFIPPDGSFDLMTYRLNTQVKPLIWVEAQVE---R----HS---RSRVEILVKARSQFKERSTATNVEIELP 174 (284)
Q Consensus 105 ~~~~~~~l~F~PPdG~F~Lm~Yr~~~~~~P~~~v~~~~~---~----~~---~~~~e~~l~~~~~~~~~~~~~~v~i~iP 174 (284)
.|-.+..|.+.+|+++|.|. +-.+.. +.+..... . .+ ..+.++.+.++...... -.|.|.=+
T Consensus 194 ~~vG~~~l~~~~~ge~~~l~-~G~d~~----v~v~r~~~~~~~~~g~~~~~~~~~~~~~itv~N~~~~~---v~v~v~d~ 265 (317)
T PF13598_consen 194 TFVGESRLPHTAPGEEFELS-FGVDPD----VRVERKLLKKEEERGFFGKSQRRTYEYTITVRNNKDEP---VTVTVEDQ 265 (317)
T ss_pred EEEEeeecCCCCCCCEEEEE-cccCCC----EEEEEEecceecccccccccEEEEEEEEEEEECCCCCC---EEEEEEeC
Confidence 34456678888888888743 444433 12211110 0 11 12455666665433322 25777777
Q ss_pred CCCCCC-cceEEecc-eeEEEeCCCCEEEEEeceecCCCeeEEEEEEE
Q 023277 175 VSSDAS-NPDVRTSM-GSASYVPEDEALIWKIRSFPGGKEYMLRAEFT 220 (284)
Q Consensus 175 lP~~~~-~~~~~~~~-G~~~~~~~~~~l~W~I~~~~~~~~~~l~~~~~ 220 (284)
+|.... ..+++... .....+...+.+.|++.--+|++ .+++..+.
T Consensus 266 iPvs~~~~I~V~~~~~~~~~~~~~~g~~~W~~~l~~g~~-~~l~~~y~ 312 (317)
T PF13598_consen 266 IPVSEDEDIKVELLEPPEPNEDEKDGILEWKVTLPPGES-RTLEFSYE 312 (317)
T ss_pred CCCCCCceEEEEEcCCCCCcccCCCCEEEEEEEECCCCE-EEEEEEEE
Confidence 776432 22232221 12356788999999998766654 34444443
No 15
>PRK09750 hypothetical protein; Provisional
Probab=24.58 E-value=62 Score=22.03 Aligned_cols=14 Identities=43% Similarity=0.769 Sum_probs=11.0
Q ss_pred EcCCCccccceEEE
Q 023277 260 EKSGYHALPWVRYI 273 (284)
Q Consensus 260 ~~~~~~~~k~vrY~ 273 (284)
++.+..|.+|+||.
T Consensus 11 ~KpGg~P~~W~r~s 24 (64)
T PRK09750 11 EKEGGTPTNWTRYS 24 (64)
T ss_pred ECCCCCccceeEec
Confidence 34667899999995
No 16
>cd06494 p23_NUDCD2_like p23-like NUD (nuclear distribution) C-like found in human NUDC domain-containing protein 2 (NUDCD2) and similar proteins. Little is known about the function of the proteins in this subgroup.
Probab=23.57 E-value=94 Score=23.07 Aligned_cols=20 Identities=30% Similarity=0.381 Sum_probs=13.7
Q ss_pred eeeEEEEEcCCCCCCcceEE
Q 023277 166 ATNVEIELPVSSDASNPDVR 185 (284)
Q Consensus 166 ~~~v~i~iPlP~~~~~~~~~ 185 (284)
.++|.|.||+|+++..-.+.
T Consensus 14 ~~eV~v~i~lp~~~~~kdv~ 33 (93)
T cd06494 14 MDEVFIEVNVPPGTRAKDVK 33 (93)
T ss_pred cCEEEEEEECCCCCceeeEE
Confidence 56888888888876544333
No 17
>PF10577 UPF0560: Uncharacterised protein family UPF0560; InterPro: IPR018890 This family of proteins has no known function.
Probab=20.03 E-value=1e+03 Score=24.99 Aligned_cols=35 Identities=20% Similarity=0.472 Sum_probs=24.4
Q ss_pred CcccccccccCCCCcccceEEEEEEEeEEEEEcCCCCEEEEE
Q 023277 10 AVTNAVSWRSEGIQYKKNEVFLDVVEHVNILVNSNGQIIRSD 51 (284)
Q Consensus 10 ~~~~~~~WR~~~~~~~~neI~vdV~E~l~~~~~~~G~v~~~~ 51 (284)
=.++++||++..+- ||=.| .|..+-.+.|++...+
T Consensus 62 yv~ns~Pw~~~rlP-----v~ssv--sL~Llp~r~a~l~lye 96 (807)
T PF10577_consen 62 YVPNSVPWKTSRLP-----VYSSV--SLSLLPERQATLWLYE 96 (807)
T ss_pred ccCCCCCccccccc-----cccce--eeeeeccCcceEEEEe
Confidence 35678899986544 55555 6777777888887775
Done!