Query 034015
Match_columns 106
No_of_seqs 101 out of 327
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 08:51:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034015.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034015hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3444 Uncharacterized conser 100.0 9.5E-35 2.1E-39 194.1 9.9 103 1-103 1-105 (121)
2 PF04628 Sedlin_N: Sedlin, N-t 100.0 1.4E-32 3E-37 189.8 7.7 92 7-104 1-100 (132)
3 KOG3487 TRAPP 20 K subunit [In 100.0 4.1E-30 8.9E-35 176.0 7.1 94 1-103 1-102 (139)
4 COG5603 TRS20 Subunit of TRAPP 99.9 1.9E-26 4.2E-31 156.3 7.1 95 1-104 1-102 (136)
5 PF04099 Sybindin: Sybindin-li 97.2 0.013 2.8E-07 40.8 11.5 86 2-88 1-95 (142)
6 KOG3368 Transport protein part 96.3 0.1 2.2E-06 36.5 9.9 90 3-102 4-100 (140)
7 COG5122 TRS23 Transport protei 95.5 0.027 5.8E-07 38.6 4.1 77 4-88 5-87 (134)
8 KOG3369 Transport protein part 94.3 0.66 1.4E-05 34.1 9.0 24 65-88 128-151 (199)
9 KOG4497 Uncharacterized conser 61.6 5.5 0.00012 32.3 1.8 53 29-86 168-220 (447)
10 PF01217 Clat_adaptor_s: Clath 58.7 53 0.0011 22.1 9.9 73 1-87 1-73 (141)
11 PF15205 PLAC9: Placenta-speci 52.9 9.3 0.0002 23.9 1.4 20 27-46 17-36 (74)
12 PF07667 DUF1600: Protein of u 39.5 19 0.00041 24.5 1.4 23 57-79 57-79 (114)
13 PF12532 DUF3732: Protein of u 35.2 46 0.00099 24.2 3.0 38 7-44 58-95 (193)
14 PF15017 AF1Q: Drug resistance 34.6 10 0.00022 24.6 -0.5 11 70-80 72-82 (87)
15 PF05017 TMP: TMP repeat; Int 33.7 22 0.00049 14.1 0.7 10 93-102 2-11 (11)
16 PF12321 DUF3634: Protein of u 30.6 61 0.0013 21.8 2.7 33 67-99 60-92 (108)
17 COG3870 Uncharacterized protei 29.4 79 0.0017 21.2 3.1 28 71-100 34-61 (109)
18 PHA01632 hypothetical protein 28.7 70 0.0015 19.3 2.5 26 77-102 13-40 (64)
19 PF04370 DUF508: Domain of unk 26.6 49 0.0011 23.5 1.7 19 69-87 44-63 (156)
20 PF03558 TBSV_P22: TBSV core p 24.3 53 0.0011 23.9 1.6 15 71-85 53-67 (189)
No 1
>KOG3444 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=9.5e-35 Score=194.12 Aligned_cols=103 Identities=57% Similarity=0.942 Sum_probs=97.2
Q ss_pred CEEEEEEEcCCCCeeEEEcCCCchhHHHHHHHHHhhhhhhhhhccCCCCCCCCCcccccccceeecCeEEEEEEecCCeE
Q 034015 1 MIACVAVVGHQNNPLYIQSFTEADDALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYLTNTKVK 80 (106)
Q Consensus 1 mi~~~aIIg~~d~PLy~~~~~~~~~~l~~~fi~h~SLDiiee~~~~~~~~~~~~~~~yLg~l~~~~~~~vygyvT~t~~K 80 (106)
|++|+|++|++|+|||+.++++.+++|++|+..|+|||+|||+....+|...+++++|||+|++.++++||||+|||++|
T Consensus 1 m~v~~av~g~kn~~lyi~s~t~~e~~L~~~y~v~~sLDVieekvn~~gkg~~tsne~fLGLLy~ted~kvYgfvtNTkVK 80 (121)
T KOG3444|consen 1 MLVCLAVAGPKNEPLYIESITPKEKELKLHYQVHLSLDVIEEKVNDPGKGERTSNELFLGLLYPTEDYKVYGFVTNTKVK 80 (121)
T ss_pred CEEEEEEEcCCCCccEEEecCcHHHHHHhHhhhhhhHHHHHHHhcCcccCccchhhhhhcccccccceeEEEEEeccEEE
Confidence 89999999999999999999988999999999999999999999887787778899999999999999999999999999
Q ss_pred EEEEEcCCC--CCchhHHHHhhhcc
Q 034015 81 FILVTTDLD--VRDADVRNVSVTIS 103 (106)
Q Consensus 81 fil~~~~~~--~~d~~Ik~ff~~i~ 103 (106)
||+++++++ +||+|||++|...|
T Consensus 81 FIlvvdssd~avreteiRsv~r~~h 105 (121)
T KOG3444|consen 81 FILVVDSSDYAVRETEIRSVFRILH 105 (121)
T ss_pred EEEEEcCCcceehhHHHHHHHHHHH
Confidence 999998764 89999999998765
No 2
>PF04628 Sedlin_N: Sedlin, N-terminal conserved region; InterPro: IPR006722 Sedlin is a 140 amino-acid protein with a putative role in endoplasmic reticulum-to-Golgi transport. Several missense mutations and deletion mutations in the SEDL gene, which result in protein truncation by frame shift, are responsible for spondyloepiphyseal dysplasia tarda, a progressive skeletal disorder (OMIM:313400). [].; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005622 intracellular; PDB: 3PR6_A 2J3W_A 1H3Q_A.
Probab=99.98 E-value=1.4e-32 Score=189.80 Aligned_cols=92 Identities=42% Similarity=0.772 Sum_probs=73.8
Q ss_pred EEcCCCCeeEEEcCCCchh------HHHHHHHHHhhhhhhhhhccCCCCCCCCCcccccccceeecCeEEEEEEecCCeE
Q 034015 7 VVGHQNNPLYIQSFTEADD------ALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYLTNTKVK 80 (106)
Q Consensus 7 IIg~~d~PLy~~~~~~~~~------~l~~~fi~h~SLDiiee~~~~~~~~~~~~~~~yLg~l~~~~~~~vygyvT~t~~K 80 (106)
|||++|+|||+++++++++ ...+||++|+|||+|||++|.+ +.++|||.|+++++++||||+|+||+|
T Consensus 1 IIg~~n~PLy~~~~~~~~~~~~~~~~~l~~~~~h~sLD~iee~~~~~------~~~~yLg~l~~~~~~~vygyvT~t~~K 74 (132)
T PF04628_consen 1 IIGPNNNPLYIRSFPSEKESSSSDARHLYQFIAHSSLDVIEEKLWKS------SSDMYLGLLDPFEDYKVYGYVTNTGIK 74 (132)
T ss_dssp EE-TTS-EEEEEEE--ST-CGHHHHHHHHHHHHHHHHHHHHHCCHCS------SSCSEEEEEEEETTEEEEEEETTT--E
T ss_pred CCCCCCcceEEEecCCCcccccchHHHHHHHHHHHHHHHHHHHHhhc------ccccccCceehhhhHHHHhhhccCcee
Confidence 7999999999999998632 2349999999999999999971 179999999999999999999999999
Q ss_pred EEEEEc--CCCCCchhHHHHhhhccc
Q 034015 81 FILVTT--DLDVRDADVRNVSVTISF 104 (106)
Q Consensus 81 fil~~~--~~~~~d~~Ik~ff~~i~~ 104 (106)
|||+++ ....+|++||+||++||-
T Consensus 75 fvl~~~~~~~~~~d~~ik~fF~~vh~ 100 (132)
T PF04628_consen 75 FVLVHDMSDNSIRDEDIKQFFKEVHE 100 (132)
T ss_dssp EEEEECGGG-S--HHHHHHHHHHHHH
T ss_pred EEEEEecccCCcchHHHHHHHHHHHH
Confidence 999998 345799999999999973
No 3
>KOG3487 consensus TRAPP 20 K subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.96 E-value=4.1e-30 Score=176.03 Aligned_cols=94 Identities=27% Similarity=0.448 Sum_probs=87.1
Q ss_pred CEEEEEEEcCCCCeeEEEcCCCc--------hhHHHHHHHHHhhhhhhhhhccCCCCCCCCCcccccccceeecCeEEEE
Q 034015 1 MIACVAVVGHQNNPLYIQSFTEA--------DDALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYG 72 (106)
Q Consensus 1 mi~~~aIIg~~d~PLy~~~~~~~--------~~~l~~~fi~h~SLDiiee~~~~~~~~~~~~~~~yLg~l~~~~~~~vyg 72 (106)
|.+|+||||+.|+|+|+.+++.. +.....||++|+|||+|||.+|.+ ++||||.+|+++++.|+|
T Consensus 1 m~~yfaIig~~d~Pvye~e~~~~~~~~~~~~~~~~LN~FI~HAaLdiVde~~W~~-------snmYLktVDkfne~~VSA 73 (139)
T KOG3487|consen 1 MTAYFAIIGHCDNPVYEMEFGCPENSKAARDDNRHLNQFIVHAALDIVDELQWTT-------SNMYLKTVDKFNELFVSA 73 (139)
T ss_pred CceEEEEEecCCCceEEeecCCCCcccccchhhHHHHHHHHHHHHHHHHHHHHHH-------HhhHHHHHHhhcceeEEE
Confidence 78999999999999999999832 345668999999999999999976 799999999999999999
Q ss_pred EEecCCeEEEEEEcCCCCCchhHHHHhhhcc
Q 034015 73 YLTNTKVKFILVTTDLDVRDADVRNVSVTIS 103 (106)
Q Consensus 73 yvT~t~~Kfil~~~~~~~~d~~Ik~ff~~i~ 103 (106)
|||++++||+++|..+ .|++||+|||+++
T Consensus 74 yvTas~i~f~mlh~~~--~~~~ik~Ffqev~ 102 (139)
T KOG3487|consen 74 YVTASHIRFIMLHINR--ADDNIKLFFQEVH 102 (139)
T ss_pred EEccCcEEEEEEeecc--ccccHHHHHHHHH
Confidence 9999999999999988 6999999999987
No 4
>COG5603 TRS20 Subunit of TRAPP, an ER-Golgi tethering complex [Cell motility and secretion]
Probab=99.93 E-value=1.9e-26 Score=156.34 Aligned_cols=95 Identities=20% Similarity=0.356 Sum_probs=86.5
Q ss_pred CEEEEEEEcCCCCeeEEEcCCCc-------hhHHHHHHHHHhhhhhhhhhccCCCCCCCCCcccccccceeecCeEEEEE
Q 034015 1 MIACVAVVGHQNNPLYIQSFTEA-------DDALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGY 73 (106)
Q Consensus 1 mi~~~aIIg~~d~PLy~~~~~~~-------~~~l~~~fi~h~SLDiiee~~~~~~~~~~~~~~~yLg~l~~~~~~~vygy 73 (106)
|-.++||||++|+|+|+.++++. ...+..||++|+|||+++.++|+. +.+|+|+|+.+.+..++||
T Consensus 1 M~~y~aIIg~KdnpVYe~e~~~~n~~~d~~~~~~ln~fiihaSlDiv~~lqwsv-------N~~Y~~~~d~f~~l~IsAY 73 (136)
T COG5603 1 MGEYLAIIGEKDNPVYEREYDPINKTSDGEYCRLLNQFIIHASLDIVVWLQWSV-------NTSYFDCLDSFGDLRISAY 73 (136)
T ss_pred CCceEEEEecCCCceeeeeecCcCcccCHHHHHHHhHHhhhhhHHHHHHHHHHh-------hhHHHHHHHhhCCeEEEEE
Confidence 77899999999999999999854 224668999999999999999976 7899999999999999999
Q ss_pred EecCCeEEEEEEcCCCCCchhHHHHhhhccc
Q 034015 74 LTNTKVKFILVTTDLDVRDADVRNVSVTISF 104 (106)
Q Consensus 74 vT~t~~Kfil~~~~~~~~d~~Ik~ff~~i~~ 104 (106)
++++|+||+++|+.. .++.+|+||||||.
T Consensus 74 i~pSgmkf~~iH~n~--s~~N~rsF~qevHe 102 (136)
T COG5603 74 IMPSGMKFLFIHQNQ--SRKNARSFLQEVHE 102 (136)
T ss_pred EccCCceEEEEeccc--hhhhHHHHHHHHHH
Confidence 999999999999876 78899999999984
No 5
>PF04099 Sybindin: Sybindin-like family ; InterPro: IPR007233 Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses. Syndecan-2 induces spine formation by recruiting intracellular vesicles toward postsynaptic sites through the interaction with synbindin []. ; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005801 cis-Golgi network; PDB: 3CUE_C 2J3T_C 2ZMV_B 2JSN_A.
Probab=97.25 E-value=0.013 Score=40.81 Aligned_cols=86 Identities=17% Similarity=0.281 Sum_probs=48.4
Q ss_pred EEEEEEEcCCCCeeEEEcCCCc---------hhHHHHHHHHHhhhhhhhhhccCCCCCCCCCcccccccceeecCeEEEE
Q 034015 2 IACVAVVGHQNNPLYIQSFTEA---------DDALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYG 72 (106)
Q Consensus 2 i~~~aIIg~~d~PLy~~~~~~~---------~~~l~~~fi~h~SLDiiee~~~~~~~~~~~~~~~yLg~l~~~~~~~vyg 72 (106)
|..+=|+++...-||-+++... +++.+.=+=.--||-.+-.++.............-+. ...++.|+++-
T Consensus 1 IyslyI~nr~G~lIy~~~~~~~~~~~~~~~~~ne~~ll~g~l~sl~~i~~klsp~~~~~~~~~~~g~~-~~~T~~yklh~ 79 (142)
T PF04099_consen 1 IYSLYIFNRSGGLIYYREWNRSKNEGQPKLSSNEYKLLAGMLHSLKAIASKLSPVDSKPNEPGSSGFE-SFETDTYKLHC 79 (142)
T ss_dssp EEEEEEE-TTS-EEEEEETSSSS--E-SSSCHHHHHHHHHHHHHHHHHHHHT-SSSSSS-SSS--SEE-EEEESS-EEEE
T ss_pred CeEEEEEeCCcceeeehhhCCCCccccCCCChhHHHHHHhhHHHHHHHHHHhCCCCcccccccceeEE-EEEeCCEEEEE
Confidence 4678899999999999998763 1233322333445666666655321111000111232 25578999999
Q ss_pred EEecCCeEEEEEEcCC
Q 034015 73 YLTNTKVKFILVTTDL 88 (106)
Q Consensus 73 yvT~t~~Kfil~~~~~ 88 (106)
|.|.||+|||++++..
T Consensus 80 ~eT~TGlKFvl~td~~ 95 (142)
T PF04099_consen 80 FETPTGLKFVLITDPN 95 (142)
T ss_dssp EE-TTS-EEEEEE-TT
T ss_pred EEcCcCcEEEEEecCC
Confidence 9999999999999875
No 6
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=96.30 E-value=0.1 Score=36.52 Aligned_cols=90 Identities=23% Similarity=0.311 Sum_probs=62.4
Q ss_pred EEEEEEcCCCCeeEEEcCCCc-------hhHHHHHHHHHhhhhhhhhhccCCCCCCCCCcccccccceeecCeEEEEEEe
Q 034015 3 ACVAVVGHQNNPLYIQSFTEA-------DDALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYLT 75 (106)
Q Consensus 3 ~~~aIIg~~d~PLy~~~~~~~-------~~~l~~~fi~h~SLDiiee~~~~~~~~~~~~~~~yLg~l~~~~~~~vygyvT 75 (106)
.-+=|-+++.+-||-++-... +++.++=|=.-.||--+-+++... +.++.++ =+++..|+++=|.|
T Consensus 4 y~~yIFdR~g~Cl~y~EW~r~~~s~~~~eee~KL~yGmlFSlkS~v~Kls~~-----d~k~~f~--sy~Ts~YklhfyeT 76 (140)
T KOG3368|consen 4 YNFYIFDRNGVCLFYREWNRTKQSGIPNEEEAKLMYGMLFSLKSFVSKLSPG-----DVKDGFL--SYKTSKYKLHFYET 76 (140)
T ss_pred EEEEEEcCCccEEEehhcccccccCCchhHHHHHHHHHHhhHHHHHHhcCCC-----CcccCee--EEeeceeEEEEEEc
Confidence 446677888888887765433 455666666677888887777643 1234443 35678899999999
Q ss_pred cCCeEEEEEEcCCCCCchhHHHHhhhc
Q 034015 76 NTKVKFILVTTDLDVRDADVRNVSVTI 102 (106)
Q Consensus 76 ~t~~Kfil~~~~~~~~d~~Ik~ff~~i 102 (106)
+||+|||+.++.+ -..+|.+.+.|
T Consensus 77 ptglk~vl~Tdpk---~~~ir~vLq~I 100 (140)
T KOG3368|consen 77 PTGLKFVLNTDPK---AGSIRDVLQYI 100 (140)
T ss_pred CCCcEEEEecCCC---cccHHHHHHHH
Confidence 9999999999763 34566665554
No 7
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=95.46 E-value=0.027 Score=38.62 Aligned_cols=77 Identities=17% Similarity=0.257 Sum_probs=51.3
Q ss_pred EEEEEcCCCCeeEEEcCCCchhHHHH--HHHHHhhhhhhhhhccCCCCCCCCCccccccc----ceeecCeEEEEEEecC
Q 034015 4 CVAVVGHQNNPLYIQSFTEADDALKL--HHIVHCSLDVVDERVNNPKKSGPTLNETFLGL----LYPTENYKVYGYLTNT 77 (106)
Q Consensus 4 ~~aIIg~~d~PLy~~~~~~~~~~l~~--~fi~h~SLDiiee~~~~~~~~~~~~~~~yLg~----l~~~~~~~vygyvT~t 77 (106)
-+-||++....+|-++|++.+.++.. -.++-++|-=|....... -+|-|. +--+..+...=|.|-|
T Consensus 5 ~~~iINksGglifqref~~~et~lnsneyLiLastlhgV~aI~tq~--------~p~~gssg~~~l~~~~f~m~I~qT~T 76 (134)
T COG5122 5 QFFIINKSGGLIFQREFGEGETELNSNEYLILASTLHGVSAILTQT--------IPLPGSSGRLVLYFRNFVMTIFQTTT 76 (134)
T ss_pred EEEEEecCCcEEEEEeccCCccccCcccEEEEeechhhhhhhhhhc--------ccCCCCCceEEEEeccEEEEEEEecC
Confidence 46789999999999999887555543 234444454444433221 112222 2235678889999999
Q ss_pred CeEEEEEEcCC
Q 034015 78 KVKFILVTTDL 88 (106)
Q Consensus 78 ~~Kfil~~~~~ 88 (106)
|+|||++.+.+
T Consensus 77 G~kFV~~~~k~ 87 (134)
T COG5122 77 GTKFVFVAEKR 87 (134)
T ss_pred CcEEEEEecCC
Confidence 99999999764
No 8
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=94.31 E-value=0.66 Score=34.06 Aligned_cols=24 Identities=21% Similarity=0.335 Sum_probs=21.8
Q ss_pred ecCeEEEEEEecCCeEEEEEEcCC
Q 034015 65 TENYKVYGYLTNTKVKFILVTTDL 88 (106)
Q Consensus 65 ~~~~~vygyvT~t~~Kfil~~~~~ 88 (106)
++.+..+.|.|-||+|||++.+..
T Consensus 128 tdtF~l~~~QTlTG~KFVvis~~~ 151 (199)
T KOG3369|consen 128 TDTFTLHIFQTLTGTKFVVIAEPG 151 (199)
T ss_pred eccEEEEEEEccCCcEEEEEecCC
Confidence 578999999999999999999864
No 9
>KOG4497 consensus Uncharacterized conserved protein WDR8, contains WD repeats [General function prediction only]
Probab=61.55 E-value=5.5 Score=32.29 Aligned_cols=53 Identities=21% Similarity=0.250 Sum_probs=42.5
Q ss_pred HHHHHHhhhhhhhhhccCCCCCCCCCcccccccceeecCeEEEEEEecCCeEEEEEEc
Q 034015 29 LHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYLTNTKVKFILVTT 86 (106)
Q Consensus 29 ~~fi~h~SLDiiee~~~~~~~~~~~~~~~yLg~l~~~~~~~vygyvT~t~~Kfil~~~ 86 (106)
++.+-|..+|-+|-.--++. +++..|...+..=+++||+|--.+|+|++---+
T Consensus 168 W~ll~~f~~dT~DltgieWs-----Pdg~~laVwd~~Leykv~aYe~~lG~k~v~wsP 220 (447)
T KOG4497|consen 168 WILLKEFKLDTIDLTGIEWS-----PDGNWLAVWDNVLEYKVYAYERGLGLKFVEWSP 220 (447)
T ss_pred HHHHHhcCCCcccccCceEC-----CCCcEEEEecchhhheeeeeeeccceeEEEecc
Confidence 67788999999986543331 157789999999999999999999999987554
No 10
>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=58.69 E-value=53 Score=22.05 Aligned_cols=73 Identities=11% Similarity=0.278 Sum_probs=43.6
Q ss_pred CEEEEEEEcCCCCeeEEEcCCCchhHHHHHHHHHhhhhhhhhhccCCCCCCCCCcccccccceeecCeEEEEEEecCCeE
Q 034015 1 MIACVAVVGHQNNPLYIQSFTEADDALKLHHIVHCSLDVVDERVNNPKKSGPTLNETFLGLLYPTENYKVYGYLTNTKVK 80 (106)
Q Consensus 1 mi~~~aIIg~~d~PLy~~~~~~~~~~l~~~fi~h~SLDiiee~~~~~~~~~~~~~~~yLg~l~~~~~~~vygyvT~t~~K 80 (106)
|+.++-|+++++++++.+-+........ +-+.....-....+ + ++ ...+...++ ..+-|...+++-
T Consensus 1 MI~~i~i~n~~G~~i~~k~y~~~~~~~~-~~~~~~~~~~~~~~---~-------~~--~~~i~~~~~-~~~vy~~~~dl~ 66 (141)
T PF01217_consen 1 MIKAILILNSQGKRILSKYYRDVSEEER-QKLFEKFIKKKSSR---N-------SK--QSPIFEHDN-YRIVYKRYSDLY 66 (141)
T ss_dssp SEEEEEEEETTSEEEEEEESSTSTSHHH-HHHHHHHHHHHHTS---S-------SS--STSEEEETT-EEEEEEEETTEE
T ss_pred CEEEEEEEcCCCCEEEehhcCCccHHHH-HHHHHHHHHHHHhc---c-------cc--cceeeeccc-ceeeeEeeccEE
Confidence 9999999999999999999965432222 21222111111111 1 01 123333445 444788888999
Q ss_pred EEEEEcC
Q 034015 81 FILVTTD 87 (106)
Q Consensus 81 fil~~~~ 87 (106)
|+++.+.
T Consensus 67 ~~~v~~~ 73 (141)
T PF01217_consen 67 FVVVGDE 73 (141)
T ss_dssp EEEEESS
T ss_pred EEEEeec
Confidence 9999974
No 11
>PF15205 PLAC9: Placenta-specific protein 9
Probab=52.88 E-value=9.3 Score=23.85 Aligned_cols=20 Identities=40% Similarity=0.607 Sum_probs=16.4
Q ss_pred HHHHHHHHhhhhhhhhhccC
Q 034015 27 LKLHHIVHCSLDVVDERVNN 46 (106)
Q Consensus 27 l~~~fi~h~SLDiiee~~~~ 46 (106)
-.-|+.+|+-||++||++-+
T Consensus 17 Cdrhmav~~RLdviEe~veK 36 (74)
T PF15205_consen 17 CDRHMAVHSRLDVIEETVEK 36 (74)
T ss_pred hHHHHHHHHHHHHHHHHHHH
Confidence 44688999999999998754
No 12
>PF07667 DUF1600: Protein of unknown function (DUF1600); InterPro: IPR011631 These proteins appear to be specific to Mycoplasma species. They are of unknown function.
Probab=39.50 E-value=19 Score=24.50 Aligned_cols=23 Identities=43% Similarity=0.587 Sum_probs=16.3
Q ss_pred cccccceeecCeEEEEEEecCCe
Q 034015 57 TFLGLLYPTENYKVYGYLTNTKV 79 (106)
Q Consensus 57 ~yLg~l~~~~~~~vygyvT~t~~ 79 (106)
+|+-..+..+.++|||..|||+-
T Consensus 57 Pf~~~~~~g~~YsVYg~~Tnt~~ 79 (114)
T PF07667_consen 57 PFLYKTDNGSTYSVYGWFTNTKD 79 (114)
T ss_pred hHheEecCCcEEEEEeeecccCC
Confidence 45544444577999999999854
No 13
>PF12532 DUF3732: Protein of unknown function (DUF3732); InterPro: IPR022205 This domain family is found in bacteria and eukaryotes, and is typically between 180 and 198 amino acids in length. There is a conserved DQP sequence motif.
Probab=35.22 E-value=46 Score=24.23 Aligned_cols=38 Identities=16% Similarity=0.246 Sum_probs=32.2
Q ss_pred EEcCCCCeeEEEcCCCchhHHHHHHHHHhhhhhhhhhc
Q 034015 7 VVGHQNNPLYIQSFTEADDALKLHHIVHCSLDVVDERV 44 (106)
Q Consensus 7 IIg~~d~PLy~~~~~~~~~~l~~~fi~h~SLDiiee~~ 44 (106)
+..+.++++|+.+.|+.++=+-+|..++.||--+=...
T Consensus 58 ~~~~~~~~~~L~~~GSgaNwl~~Hla~fLaLH~~f~~~ 95 (193)
T PF12532_consen 58 VFDRKNRPIPLREMGSGANWLAYHLALFLALHEFFAKN 95 (193)
T ss_pred EecCCCCeEeHHhcCChHHHHHHHHHHHHHHHHHHHhc
Confidence 47889999999999998888889999999997764443
No 14
>PF15017 AF1Q: Drug resistance and apoptosis regulator
Probab=34.61 E-value=10 Score=24.59 Aligned_cols=11 Identities=27% Similarity=0.498 Sum_probs=9.2
Q ss_pred EEEEEecCCeE
Q 034015 70 VYGYLTNTKVK 80 (106)
Q Consensus 70 vygyvT~t~~K 80 (106)
=-||+|++|+|
T Consensus 72 ~gGWITPsNIk 82 (87)
T PF15017_consen 72 GGGWITPSNIK 82 (87)
T ss_pred CCccccchhhh
Confidence 45899999987
No 15
>PF05017 TMP: TMP repeat; InterPro: IPR007713 This short repeat consists of the motif WXXh where X can be any residue and h is a hydrophobic residue. The repeat is named TMP after its occurrence in the tape measure protein (TMP). Tape measure protein is a component of phage tail and probably forms a beta-helix. Truncated forms of TMP lead to shortened tail fibres []. This repeat is also found in non-phage proteins where it may play a structural role.
Probab=33.74 E-value=22 Score=14.14 Aligned_cols=10 Identities=0% Similarity=0.162 Sum_probs=6.7
Q ss_pred hhHHHHhhhc
Q 034015 93 ADVRNVSVTI 102 (106)
Q Consensus 93 ~~Ik~ff~~i 102 (106)
+.||++|..|
T Consensus 2 n~Ik~~~s~v 11 (11)
T PF05017_consen 2 NGIKSFFSGV 11 (11)
T ss_pred chHHHHhhcC
Confidence 3588887653
No 16
>PF12321 DUF3634: Protein of unknown function (DUF3634); InterPro: IPR022090 This family of proteins is found in bacteria. Proteins in this family are typically between 103 and 114 amino acids in length.
Probab=30.64 E-value=61 Score=21.81 Aligned_cols=33 Identities=15% Similarity=0.096 Sum_probs=23.4
Q ss_pred CeEEEEEEecCCeEEEEEEcCCCCCchhHHHHh
Q 034015 67 NYKVYGYLTNTKVKFILVTTDLDVRDADVRNVS 99 (106)
Q Consensus 67 ~~~vygyvT~t~~Kfil~~~~~~~~d~~Ik~ff 99 (106)
...+.||.+.+++|+..--+-..---+.|||+|
T Consensus 60 ~G~ik~~r~~~g~rL~fS~~ip~~v~QriRNvf 92 (108)
T PF12321_consen 60 RGTIKVYRQRGGVRLHFSRSIPKKVQQRIRNVF 92 (108)
T ss_pred cEEEEEEEeCCceEEEEeCCCCHHHhhhhhhcC
Confidence 567899999999998776543221234688886
No 17
>COG3870 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.38 E-value=79 Score=21.24 Aligned_cols=28 Identities=21% Similarity=0.336 Sum_probs=20.4
Q ss_pred EEEEecCCeEEEEEEcCCCCCchhHHHHhh
Q 034015 71 YGYLTNTKVKFILVTTDLDVRDADVRNVSV 100 (106)
Q Consensus 71 ygyvT~t~~Kfil~~~~~~~~d~~Ik~ff~ 100 (106)
-||...+|..|++.+++. +=+++|+...
T Consensus 34 GGFlkaGNTTfliGved~--~vd~~~s~Ik 61 (109)
T COG3870 34 GGFLKAGNTTFLIGVEDD--RVDALRSLIK 61 (109)
T ss_pred CceeecCCeEEEEecccc--hhHHHHHHHH
Confidence 368999999999999875 4445555443
No 18
>PHA01632 hypothetical protein
Probab=28.73 E-value=70 Score=19.29 Aligned_cols=26 Identities=15% Similarity=0.336 Sum_probs=20.3
Q ss_pred CCeEEEEEEcCCC--CCchhHHHHhhhc
Q 034015 77 TKVKFILVTTDLD--VRDADVRNVSVTI 102 (106)
Q Consensus 77 t~~Kfil~~~~~~--~~d~~Ik~ff~~i 102 (106)
-++|+-+++++.| +.++++|.+.-++
T Consensus 13 lhikiyilieqvp~kpteeelrkvlpki 40 (64)
T PHA01632 13 LHIKIYILIEQVPQKPTEEELRKVLPKI 40 (64)
T ss_pred EEEEEEEehhhcCCCCCHHHHHHHHHHH
Confidence 3688888888744 7899999887665
No 19
>PF04370 DUF508: Domain of unknown function (DUF508) ; InterPro: IPR007465 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=26.55 E-value=49 Score=23.50 Aligned_cols=19 Identities=53% Similarity=0.789 Sum_probs=15.6
Q ss_pred EEEE-EEecCCeEEEEEEcC
Q 034015 69 KVYG-YLTNTKVKFILVTTD 87 (106)
Q Consensus 69 ~vyg-yvT~t~~Kfil~~~~ 87 (106)
+..| |||--++|||++|-+
T Consensus 44 k~sgK~V~MVhVKFilLh~D 63 (156)
T PF04370_consen 44 KSSGKYVTMVHVKFILLHRD 63 (156)
T ss_pred cccccEEEEEEEEEEEEehH
Confidence 4455 888889999999975
No 20
>PF03558 TBSV_P22: TBSV core protein P21/P22; InterPro: IPR005332 Two small nested genes (p19 and p22) are located near the 3' end of the genome of tomato bushy stunt virus (TBSV) - the p19 gene encodes a soluble protein, whereas the p22 gene specifies a membrane-associated protein. p22 is required for cell-to-cell movement in all plants tested [].; GO: 0019028 viral capsid
Probab=24.32 E-value=53 Score=23.91 Aligned_cols=15 Identities=33% Similarity=0.718 Sum_probs=12.7
Q ss_pred EEEEecCCeEEEEEE
Q 034015 71 YGYLTNTKVKFILVT 85 (106)
Q Consensus 71 ygyvT~t~~Kfil~~ 85 (106)
-||.|.+++||++.=
T Consensus 53 ggY~t~~~Vr~~itP 67 (189)
T PF03558_consen 53 GGYITIRDVRFVITP 67 (189)
T ss_pred cceeeceeeEEEEee
Confidence 379999999999854
Done!