Query 036677
Match_columns 78
No_of_seqs 114 out of 409
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 04:25:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036677.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036677hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0934 Clathrin adaptor compl 100.0 5.2E-31 1.1E-35 183.7 4.4 65 1-78 31-95 (145)
2 COG5030 APS2 Clathrin adaptor 100.0 5E-29 1.1E-33 174.6 5.4 65 1-78 31-95 (152)
3 KOG0936 Clathrin adaptor compl 99.9 1.2E-28 2.6E-33 175.7 4.8 71 1-78 31-101 (182)
4 KOG0935 Clathrin adaptor compl 99.9 3.6E-22 7.7E-27 138.2 5.3 64 2-78 32-96 (143)
5 PF01217 Clat_adaptor_s: Clath 99.6 2.4E-15 5.2E-20 100.7 5.0 64 2-78 32-95 (141)
6 KOG3343 Vesicle coat complex C 82.8 2.9 6.4E-05 30.4 4.5 40 31-75 60-99 (175)
7 KOG0937 Adaptor complexes medi 72.8 8.9 0.00019 31.3 5.0 41 33-78 53-93 (424)
8 KOG2635 Medium subunit of clat 63.6 14 0.00031 30.7 4.5 49 15-76 44-92 (512)
9 KOG2740 Clathrin-associated pr 62.9 8.9 0.00019 31.2 3.2 32 47-78 64-95 (418)
10 PF11447 DUF3201: Protein of u 34.8 31 0.00066 24.7 1.9 28 46-76 66-93 (150)
11 PF15001 AP-5_subunit_s1: AP-5 32.1 1.3E+02 0.0029 22.0 4.9 38 32-74 103-140 (189)
12 PF10538 ITAM_Cys-rich: Immuno 29.3 61 0.0013 16.6 2.0 19 36-54 4-22 (24)
13 PF11453 DUF2950: Protein of u 25.1 43 0.00093 26.0 1.4 22 56-77 107-128 (271)
No 1
>KOG0934 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.96 E-value=5.2e-31 Score=183.74 Aligned_cols=65 Identities=49% Similarity=0.996 Sum_probs=63.8
Q ss_pred CHHHHHHHHHhCCCCceeeeecCCCCCCccccceEEeecccceeeeceEEEEEeCCCCChhHHHHHHHHHHhhhccCC
Q 036677 1 VIRELSGIILTRSPKLCNFVEWNGGLPTSIIFNTKCYPRENVIIYSGLYFCMCVDPDDNELEILDIIHHYVEILDLYF 78 (78)
Q Consensus 1 i~~ei~~~il~R~~~~cnf~e~~~~k~~~~~~~~iVYRr~~~~~YAsLyFi~~vD~~eNEL~~LelIh~fVE~LD~yF 78 (78)
++||+.+.|++|+|++|||+||+++| +|||| ||||||++|++.+||||++||+||+|||+||+||
T Consensus 31 i~re~i~~~Lar~pk~csfie~kd~k--------vVyrr-----yasl~f~~~v~~~dNEL~~LE~IH~~vE~lDkYF 95 (145)
T KOG0934|consen 31 IERELIKSVLARKPKMCSFIEYKDEK--------VVYRR-----YASLFFCVGVEDNDNELAILEFIHNYVELLDKYF 95 (145)
T ss_pred HHHHHHHHHHhCCcccccchhccCce--------ehhhh-----hhhEEEEEEEecCCchhhHHHHHHHHHHHHHHHh
Confidence 47999999999999999999999999 99999 9999999999999999999999999999999998
No 2
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=99.95 E-value=5e-29 Score=174.57 Aligned_cols=65 Identities=48% Similarity=0.812 Sum_probs=63.3
Q ss_pred CHHHHHHHHHhCCCCceeeeecCCCCCCccccceEEeecccceeeeceEEEEEeCCCCChhHHHHHHHHHHhhhccCC
Q 036677 1 VIRELSGIILTRSPKLCNFVEWNGGLPTSIIFNTKCYPRENVIIYSGLYFCMCVDPDDNELEILDIIHHYVEILDLYF 78 (78)
Q Consensus 1 i~~ei~~~il~R~~~~cnf~e~~~~k~~~~~~~~iVYRr~~~~~YAsLyFi~~vD~~eNEL~~LelIh~fVE~LD~yF 78 (78)
++++|+++|++|+||+|||+|+++.| +|||| ||||||++|||++||||++||+||.|||+||+||
T Consensus 31 li~~i~~lIs~R~~ke~N~~e~k~~k--------iVYrr-----YA~LyF~f~Vd~~dnEl~iL~lIh~FVE~lDr~F 95 (152)
T COG5030 31 LIADIYELISARKPKESNFIEGKNEK--------IVYRR-----YATLYFVFGVDNDDNELIILELIHNFVEILDRFF 95 (152)
T ss_pred HHHHHHHHHHcCCchhcccccccCcE--------EEeee-----cCcEEEEEEEcCCCCcchHHHHHHHHHHHHHHHh
Confidence 47899999999999999999999988 99999 9999999999999999999999999999999998
No 3
>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.95 E-value=1.2e-28 Score=175.74 Aligned_cols=71 Identities=39% Similarity=0.645 Sum_probs=66.0
Q ss_pred CHHHHHHHHHhCCCCceeeeecCCCCCCccccceEEeecccceeeeceEEEEEeCCCCChhHHHHHHHHHHhhhccCC
Q 036677 1 VIRELSGIILTRSPKLCNFVEWNGGLPTSIIFNTKCYPRENVIIYSGLYFCMCVDPDDNELEILDIIHHYVEILDLYF 78 (78)
Q Consensus 1 i~~ei~~~il~R~~~~cnf~e~~~~k~~~~~~~~iVYRr~~~~~YAsLyFi~~vD~~eNEL~~LelIh~fVE~LD~yF 78 (78)
++|++++++++|++..|||+|..+.- .+.++|+|||+ ||+|||++++|.+||||++||+||+|||+|||||
T Consensus 31 lir~vf~lvs~R~~n~~nFLe~~~l~--g~~d~rlIYrh-----YATLYFvfvvD~sEsEL~iLDLIQvfVEtLDkCF 101 (182)
T KOG0936|consen 31 LIREVFHLVSKRPDNVCNFLEGNSLI--GGSDNRLIYRH-----YATLYFVFVVDSSESELGILDLIQVFVETLDKCF 101 (182)
T ss_pred HHHHHHHHHHcCCchHhhhhcccccc--CCccceeehhe-----eeeEEEEEEEcCCcchhHHHHHHHHHHHHHHHHH
Confidence 57999999999999999999877543 45789999999 9999999999999999999999999999999998
No 4
>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.86 E-value=3.6e-22 Score=138.24 Aligned_cols=64 Identities=48% Similarity=0.893 Sum_probs=59.1
Q ss_pred HHHHHHHHHhCCCCceeeeecCCCCCCccccceEEee-cccceeeeceEEEEEeCCCCChhHHHHHHHHHHhhhccCC
Q 036677 2 IRELSGIILTRSPKLCNFVEWNGGLPTSIIFNTKCYP-RENVIIYSGLYFCMCVDPDDNELEILDIIHHYVEILDLYF 78 (78)
Q Consensus 2 ~~ei~~~il~R~~~~cnf~e~~~~k~~~~~~~~iVYR-r~~~~~YAsLyFi~~vD~~eNEL~~LelIh~fVE~LD~yF 78 (78)
+.||++++.+|+.|.-||++.++.| ++|| | ||+|||++|||..||||++||.||.|||+||.||
T Consensus 32 ~~~vh~lvs~Rd~K~~~~~~~~~~~--------~~~~rr-----yagLyf~~~vd~tDnelayLe~IHlFVEvLd~fF 96 (143)
T KOG0935|consen 32 IEEVHALVTVRDAKHTNFVEFRNFK--------IIYRRR-----YAGLYFCICVDVTDNELAYLEHIHLFVEVLDEFF 96 (143)
T ss_pred HHHHHHHHhhccchhhhheeeeece--------EEEEEe-----eCCEEEEEEEecCCchHHHHHHHHHHHHHHHHHh
Confidence 6799999999999998888888777 6655 7 9999999999999999999999999999999987
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=99.58 E-value=2.4e-15 Score=100.70 Aligned_cols=64 Identities=34% Similarity=0.564 Sum_probs=60.7
Q ss_pred HHHHHHHHHhCCCCceeeeecCCCCCCccccceEEeecccceeeeceEEEEEeCCCCChhHHHHHHHHHHhhhccCC
Q 036677 2 IRELSGIILTRSPKLCNFVEWNGGLPTSIIFNTKCYPRENVIIYSGLYFCMCVDPDDNELEILDIIHHYVEILDLYF 78 (78)
Q Consensus 2 ~~ei~~~il~R~~~~cnf~e~~~~k~~~~~~~~iVYRr~~~~~YAsLyFi~~vD~~eNEL~~LelIh~fVE~LD~yF 78 (78)
.+++.+.+.+|+++.|+++++++++ +|||+ |+.|||++++|.++|||+++|++|.+||+|+.||
T Consensus 32 ~~~~~~~~~~~~~~~~~i~~~~~~~--------~vy~~-----~~dl~~~~v~~~~eNel~~~e~l~~~v~~l~~~~ 95 (141)
T PF01217_consen 32 FEKFIKKKSSRNSKQSPIFEHDNYR--------IVYKR-----YSDLYFVVVGDENENELLLLEFLHRLVEVLDDYF 95 (141)
T ss_dssp HHHHHHHHHTSSSSSTSEEEETTEE--------EEEEE-----ETTEEEEEEESSTSBHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhcccccceeeecccce--------eeeEe-----eccEEEEEEeecccchHHHHHHHHHhhhhhhhhh
Confidence 4677889999999999999999999 99999 9999999999999999999999999999999886
No 6
>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=82.79 E-value=2.9 Score=30.44 Aligned_cols=40 Identities=23% Similarity=0.319 Sum_probs=33.7
Q ss_pred ccceEEeecccceeeeceEEEEEeCCCCChhHHHHHHHHHHhhhc
Q 036677 31 IFNTKCYPRENVIIYSGLYFCMCVDPDDNELEILDIIHHYVEILD 75 (78)
Q Consensus 31 ~~~~iVYRr~~~~~YAsLyFi~~vD~~eNEL~~LelIh~fVE~LD 75 (78)
.++.+|||- +--|+|-+.--..||||......+.+-+.|+
T Consensus 60 dg~~vvYk~-----~~Dl~fyv~G~~~ENEl~L~svL~~l~dal~ 99 (175)
T KOG3343|consen 60 DGNTVVYKS-----VIDLHFYVVGSEEENELMLMSVLTCLFDALS 99 (175)
T ss_pred cCcEEEEEe-----cccEEEEEecCcchhHHHHHHHHHHHHHHHH
Confidence 356699999 9999999999999999999888877766654
No 7
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=72.82 E-value=8.9 Score=31.30 Aligned_cols=41 Identities=15% Similarity=0.248 Sum_probs=36.3
Q ss_pred ceEEeecccceeeeceEEEEEeCCCCChhHHHHHHHHHHhhhccCC
Q 036677 33 NTKCYPRENVIIYSGLYFCMCVDPDDNELEILDIIHHYVEILDLYF 78 (78)
Q Consensus 33 ~~iVYRr~~~~~YAsLyFi~~vD~~eNEL~~LelIh~fVE~LD~yF 78 (78)
...+|=+ ...||+++++-.+.|-..++++++..|+++-.||
T Consensus 53 ~~~~~ik-----~s~lylv~~~~~n~~a~~v~~~l~~~~~v~~~y~ 93 (424)
T KOG0937|consen 53 SRFIHIK-----HSNLYLVAGTRPNVSAALVLSFLYAVADVFGDYL 93 (424)
T ss_pred ceEEEEe-----ecceEEEEEeccCCCHHHHHHHHHHHHHHHHHHh
Confidence 3467777 9999999999999999999999999999988776
No 8
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=63.57 E-value=14 Score=30.75 Aligned_cols=49 Identities=22% Similarity=0.338 Sum_probs=39.9
Q ss_pred CceeeeecCCCCCCccccceEEeecccceeeeceEEEEEeCCCCChhHHHHHHHHHHhhhcc
Q 036677 15 KLCNFVEWNGGLPTSIIFNTKCYPRENVIIYSGLYFCMCVDPDDNELEILDIIHHYVEILDL 76 (78)
Q Consensus 15 ~~cnf~e~~~~k~~~~~~~~iVYRr~~~~~YAsLyFi~~vD~~eNEL~~LelIh~fVE~LD~ 76 (78)
++=-|+|-...+ .||+- .-.||.+++...+-|-|.-|+..+.|..+.-.
T Consensus 44 ~qhT~vEt~~VR--------YVYqP-----~d~lY~vLITtk~SNIleDl~TL~Lfskvipe 92 (512)
T KOG2635|consen 44 KQHTFVETDSVR--------YVYQP-----LDNLYIVLITTKQSNILEDLETLRLFSKVIPE 92 (512)
T ss_pred CCccEEecccEE--------EEEEe-----cccEEEEEEeccccchhhHHHHHHHHHHhchh
Confidence 344566666666 99999 99999999999999999999999998866443
No 9
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=62.93 E-value=8.9 Score=31.23 Aligned_cols=32 Identities=25% Similarity=0.635 Sum_probs=29.0
Q ss_pred ceEEEEEeCCCCChhHHHHHHHHHHhhhccCC
Q 036677 47 GLYFCMCVDPDDNELEILDIIHHYVEILDLYF 78 (78)
Q Consensus 47 sLyFi~~vD~~eNEL~~LelIh~fVE~LD~yF 78 (78)
.+|||.++..+--.|-+.|+.|+.|.+|-.||
T Consensus 64 ~i~~~~~st~e~pPL~~iefL~rv~dv~~eyF 95 (418)
T KOG2740|consen 64 LIFFCAVSTVETPPLMVIEFLHRVVDVLLEYF 95 (418)
T ss_pred CcEEEEEEeccCCChhHHHHHHHHHHHHHHHh
Confidence 68999999887779999999999999998887
No 10
>PF11447 DUF3201: Protein of unknown function (DUF3201); InterPro: IPR024505 This archaeal family of proteins has no known function.; PDB: 1YB3_A.
Probab=34.77 E-value=31 Score=24.65 Aligned_cols=28 Identities=14% Similarity=0.428 Sum_probs=21.1
Q ss_pred eceEEEEEeCCCCChhHHHHHHHHHHhhhcc
Q 036677 46 SGLYFCMCVDPDDNELEILDIIHHYVEILDL 76 (78)
Q Consensus 46 AsLyFi~~vD~~eNEL~~LelIh~fVE~LD~ 76 (78)
-|.||++++..++ ...|++..|++..-|
T Consensus 66 q~~YFvfav~kE~---is~~Fv~~fl~~F~k 93 (150)
T PF11447_consen 66 QGFYFVFAVPKEK---ISEEFVKEFLRKFPK 93 (150)
T ss_dssp TEEEEEEEEEGGG-----HHHHHHHHHH-SE
T ss_pred ceEEEEEEeeHHH---hhHHHHHHHHHhCch
Confidence 4789999999876 778999999887654
No 11
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=32.08 E-value=1.3e+02 Score=21.99 Aligned_cols=38 Identities=16% Similarity=0.323 Sum_probs=29.0
Q ss_pred cceEEeecccceeeeceEEEEEeCCCCChhHHHHHHHHHHhhh
Q 036677 32 FNTKCYPRENVIIYSGLYFCMCVDPDDNELEILDIIHHYVEIL 74 (78)
Q Consensus 32 ~~~iVYRr~~~~~YAsLyFi~~vD~~eNEL~~LelIh~fVE~L 74 (78)
+..+|+.. -.++-|..+.|..||=+.+=-+.+.++-.|
T Consensus 103 ~k~vvW~~-----v~~l~ftLVce~hEN~lLa~~~L~~~~~~l 140 (189)
T PF15001_consen 103 PKIVVWLG-----VGSLCFTLVCEPHENRLLAENTLRLFIRHL 140 (189)
T ss_pred CcEEEeec-----cCCEEEEEEecCchhHHHHHHHHHHHHHHH
Confidence 44677888 999999999999999776655655555443
No 12
>PF10538 ITAM_Cys-rich: Immunoreceptor tyrosine-based activation motif; InterPro: IPR012316 Signal transduction by T and B cell antigen receptors and certain receptors for Ig Fc regions involves a conserved sequence motif, termed an immunoreceptor tyrosine-based activation motif (ITAM). It is also found in the cytoplasmic domain of the apoptosis receptor. Phosphorylation of the two ITAM tyrosines is a critical event in signal transduction. All (p)2ITAMs, but not their nonphosphorylated counterparts, induced extensive protein tyrosine phosphorylation in permeabilised cells. After binding of the ligand via an SH2 domain, phosphorylation of the two conserved tyrosines of ITAM creates binding sites for downstream signalling molecules and thus enables the initiation of signalling events. This phosphorylation was found to reflect activation of the src family kinases Lyn and Syk. Different ITAMs may preferentially activate distinct signalling pathways as a consequence of distinct SH2 effector binding preference [, ]. Furthermore, in viruses, ITAMs may play key roles in viral pathogenesis by regulating viral clearance, immune cell activation, immune cell recruitment through binding of cellular kinases and thereby down regulate their function []. This motif can be found in one to three copies and in association with the Ig-like domain. Proteins currently known to contain an ITAM motif are: Mammalian alpha and beta immunoglobulin proteins, TCR gamma receptors, FCR gamma receptors subunits, CD3 chains receptors and NFAT activation molecule. Hantavirus cytoplasmic elements. ; GO: 0007165 signal transduction
Probab=29.33 E-value=61 Score=16.59 Aligned_cols=19 Identities=21% Similarity=0.541 Sum_probs=14.7
Q ss_pred EeecccceeeeceEEEEEe
Q 036677 36 CYPRENVIIYSGLYFCMCV 54 (78)
Q Consensus 36 VYRr~~~~~YAsLyFi~~v 54 (78)
.||++..+.|-|=.+|..+
T Consensus 4 ~Yr~L~~FrYksrCyi~~v 22 (24)
T PF10538_consen 4 CYRTLSLFRYKSRCYIFTV 22 (24)
T ss_pred hheeeeeeEEeeeEEEEEE
Confidence 5888888889888877654
No 13
>PF11453 DUF2950: Protein of unknown function (DUF2950); InterPro: IPR021556 This is a bacterial family of uncharacterised proteins.
Probab=25.13 E-value=43 Score=25.96 Aligned_cols=22 Identities=27% Similarity=0.413 Sum_probs=19.2
Q ss_pred CCCChhHHHHHHHHHHhhhccC
Q 036677 56 PDDNELEILDIIHHYVEILDLY 77 (78)
Q Consensus 56 ~~eNEL~~LelIh~fVE~LD~y 77 (78)
-..|||++++..|.||+.-..|
T Consensus 107 IGRNEL~aI~~~~ayvdAQ~eY 128 (271)
T PF11453_consen 107 IGRNELAAIQTLLAYVDAQREY 128 (271)
T ss_pred cchhHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999986655
Done!