Query 035597
Match_columns 86
No_of_seqs 100 out of 374
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 04:22:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035597.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035597hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5030 APS2 Clathrin adaptor 99.9 4.8E-24 1E-28 154.5 5.0 66 13-78 52-138 (152)
2 KOG0936 Clathrin adaptor compl 99.9 1.1E-22 2.5E-27 150.1 4.6 69 13-81 58-147 (182)
3 KOG0934 Clathrin adaptor compl 99.9 9.3E-23 2E-27 147.0 2.7 67 13-79 52-139 (145)
4 KOG0935 Clathrin adaptor compl 99.9 1.6E-22 3.5E-27 144.8 3.4 65 16-80 56-141 (143)
5 PF01217 Clat_adaptor_s: Clath 99.7 5.8E-17 1.3E-21 110.7 5.3 68 14-81 53-141 (141)
6 KOG3343 Vesicle coat complex C 97.1 0.0012 2.6E-08 49.4 5.1 63 15-77 61-145 (175)
7 KOG2740 Clathrin-associated pr 96.3 0.0037 7.9E-08 51.8 3.2 47 22-68 65-128 (418)
8 KOG0938 Adaptor complexes medi 90.4 0.42 9.1E-06 40.0 4.1 56 22-77 62-134 (446)
9 KOG0937 Adaptor complexes medi 88.1 0.65 1.4E-05 38.9 3.7 57 22-79 63-136 (424)
10 PF15001 AP-5_subunit_s1: AP-5 74.9 14 0.0003 27.9 6.2 65 6-70 94-180 (189)
11 COG5541 RET3 Vesicle coat comp 61.4 23 0.0005 26.9 5.0 49 29-77 86-152 (187)
12 PF00780 CNH: CNH domain; Int 38.2 34 0.00074 24.5 2.6 21 10-30 226-246 (275)
13 COG1993 PII-like signaling pro 34.8 22 0.00048 25.0 1.2 41 10-63 55-96 (109)
14 PF11447 DUF3201: Protein of u 32.8 28 0.0006 25.8 1.5 57 22-83 68-130 (150)
15 KOG2635 Medium subunit of clat 28.7 1.2E+02 0.0026 26.4 4.7 49 13-61 51-120 (512)
16 PF01172 SBDS: Shwachman-Bodia 24.2 26 0.00056 23.0 0.0 17 53-69 71-87 (91)
17 PF11453 DUF2950: Protein of u 23.9 61 0.0013 25.9 2.1 23 30-52 107-129 (271)
18 TIGR03358 VI_chp_5 type VI sec 21.6 92 0.002 22.9 2.5 17 12-28 7-34 (159)
19 cd09030 DUF1425 Putative perip 21.3 1.3E+02 0.0027 19.4 2.9 18 8-25 40-57 (101)
No 1
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=99.89 E-value=4.8e-24 Score=154.47 Aligned_cols=66 Identities=24% Similarity=0.261 Sum_probs=62.0
Q ss_pred CCCceeEEE----eeeEEEEcCCCchhhhHHHHHHHHHHhhhhh-----------------hhheeecceeeeeechhhh
Q 035597 13 PKPLKLHFE----FPRVVSMRTCGNKLAILKFIYLLVETADCGI-----------------VIVEKVMDGCMAGTSKSNI 71 (86)
Q Consensus 13 ~~~~~~~y~----l~fi~~VD~~dNELa~LE~IH~fVE~LDkyF-----------------ILDEmil~Gev~ETsk~~I 71 (86)
.++.||+|| |||++|||.+||||++||+||+|||+||+|| |||||++||+++||||++|
T Consensus 52 ~k~~kiVYrrYA~LyF~f~Vd~~dnEl~iL~lIh~FVE~lDr~FgnVCELdlIFNF~kv~~ILdE~i~gG~i~Es~~~~v 131 (152)
T COG5030 52 GKNEKIVYRRYATLYFVFGVDNDDNELIILELIHNFVEILDRFFGNVCELDLIFNFQKVYAILDEMILGGEIIESSKNEV 131 (152)
T ss_pred ccCcEEEeeecCcEEEEEEEcCCCCcchHHHHHHHHHHHHHHHhccceeeEeEeeHHHHHHHHHHHHhCCeeeecCHHHH
Confidence 345699999 9999999999999999999999999999999 9999999999999999999
Q ss_pred cccchhc
Q 035597 72 LTPDKTD 78 (86)
Q Consensus 72 L~~i~~~ 78 (86)
++++...
T Consensus 132 l~~v~~l 138 (152)
T COG5030 132 LEHVYAL 138 (152)
T ss_pred HHHHHHH
Confidence 9887655
No 2
>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.87 E-value=1.1e-22 Score=150.05 Aligned_cols=69 Identities=23% Similarity=0.318 Sum_probs=66.1
Q ss_pred CCCceeEEE----eeeEEEEcCCCchhhhHHHHHHHHHHhhhhh-----------------hhheeecceeeeeechhhh
Q 035597 13 PKPLKLHFE----FPRVVSMRTCGNKLAILKFIYLLVETADCGI-----------------VIVEKVMDGCMAGTSKSNI 71 (86)
Q Consensus 13 ~~~~~~~y~----l~fi~~VD~~dNELa~LE~IH~fVE~LDkyF-----------------ILDEmil~Gev~ETsk~~I 71 (86)
+++.||.|| |||++|+|.+||||++||+||.|||+||||| ||+|+++||++.|||.++|
T Consensus 58 ~~d~rlIYrhYATLYFvfvvD~sEsEL~iLDLIQvfVEtLDkCF~nVcELDliF~~~k~h~iL~EiV~GGmVlETn~neI 137 (182)
T KOG0936|consen 58 GSDNRLIYRHYATLYFVFVVDSSESELGILDLIQVFVETLDKCFENVCELDLIFNWQKVHAILAEIVMGGMVLETNMNEI 137 (182)
T ss_pred CccceeehheeeeEEEEEEEcCCcchhHHHHHHHHHHHHHHHHHHhhhhhhheeeHHHHHHHHHHHHhCCeEEeccHHHH
Confidence 489999999 9999999999999999999999999999999 9999999999999999999
Q ss_pred cccchhcchh
Q 035597 72 LTPDKTDGEN 81 (86)
Q Consensus 72 L~~i~~~~~~ 81 (86)
+.++.++.|.
T Consensus 138 v~av~~~nkl 147 (182)
T KOG0936|consen 138 VAAVDEQNKL 147 (182)
T ss_pred HHHHHHhchh
Confidence 9999887764
No 3
>KOG0934 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.86 E-value=9.3e-23 Score=147.01 Aligned_cols=67 Identities=28% Similarity=0.306 Sum_probs=63.6
Q ss_pred CCCceeEEE----eeeEEEEcCCCchhhhHHHHHHHHHHhhhhh-----------------hhheeecceeeeeechhhh
Q 035597 13 PKPLKLHFE----FPRVVSMRTCGNKLAILKFIYLLVETADCGI-----------------VIVEKVMDGCMAGTSKSNI 71 (86)
Q Consensus 13 ~~~~~~~y~----l~fi~~VD~~dNELa~LE~IH~fVE~LDkyF-----------------ILDEmil~Gev~ETsk~~I 71 (86)
.++.|+||| |+|++||+.+||||++||+||+|||+||+|| ||||++++|+++|+||+.+
T Consensus 52 ~kd~kvVyrryasl~f~~~v~~~dNEL~~LE~IH~~vE~lDkYFg~VCELDiiFNfekay~ILde~~~~g~~~e~~k~~~ 131 (145)
T KOG0934|consen 52 YKDEKVVYRRYASLFFCVGVEDNDNELAILEFIHNYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEIQETSKNDV 131 (145)
T ss_pred ccCceehhhhhhhEEEEEEEecCCchhhHHHHHHHHHHHHHHHhccceeeEEEEehHhHHHHHHHHhcCcchHhhhcccH
Confidence 367899999 9999999999999999999999999999999 9999999999999999999
Q ss_pred cccchhcc
Q 035597 72 LTPDKTDG 79 (86)
Q Consensus 72 L~~i~~~~ 79 (86)
++.+.++|
T Consensus 132 ~~~i~~ad 139 (145)
T KOG0934|consen 132 LKAIAQAD 139 (145)
T ss_pred HHHHHHhh
Confidence 99987765
No 4
>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.86 E-value=1.6e-22 Score=144.79 Aligned_cols=65 Identities=23% Similarity=0.196 Sum_probs=59.5
Q ss_pred ceeEEE----eeeEEEEcCCCchhhhHHHHHHHHHHhhhhh-----------------hhheeecceeeeeechhhhccc
Q 035597 16 LKLHFE----FPRVVSMRTCGNKLAILKFIYLLVETADCGI-----------------VIVEKVMDGCMAGTSKSNILTP 74 (86)
Q Consensus 16 ~~~~y~----l~fi~~VD~~dNELa~LE~IH~fVE~LDkyF-----------------ILDEmil~Gev~ETsk~~IL~~ 74 (86)
..+.|| |||++|||..|||+++||.||+|||+||.|| |+|||++|||++||||+.++++
T Consensus 56 ~~~~~rryagLyf~~~vd~tDnelayLe~IHlFVEvLd~fF~NVCELDlvFNFyKVy~i~DEm~l~GEi~Etsk~~vler 135 (143)
T KOG0935|consen 56 KIIYRRRYAGLYFCICVDVTDNELAYLEHIHLFVEVLDEFFHNVCELDLVFNFYKVYTIVDEMFLAGEIRETSKTKVLER 135 (143)
T ss_pred eEEEEEeeCCEEEEEEEecCCchHHHHHHHHHHHHHHHHHhccccceeeeeeeeeHHHHHHHHHHhhhhhhhhHHHHHHH
Confidence 345554 9999999999999999999999999999999 9999999999999999999999
Q ss_pred chhcch
Q 035597 75 DKTDGE 80 (86)
Q Consensus 75 i~~~~~ 80 (86)
+...++
T Consensus 136 l~~L~~ 141 (143)
T KOG0935|consen 136 LLMLQS 141 (143)
T ss_pred HHHHhc
Confidence 876553
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=99.68 E-value=5.8e-17 Score=110.67 Aligned_cols=68 Identities=22% Similarity=0.249 Sum_probs=62.4
Q ss_pred CCceeEEE----eeeEEEEcCCCchhhhHHHHHHHHHHhhhhh-----------------hhheeecceeeeeechhhhc
Q 035597 14 KPLKLHFE----FPRVVSMRTCGNKLAILKFIYLLVETADCGI-----------------VIVEKVMDGCMAGTSKSNIL 72 (86)
Q Consensus 14 ~~~~~~y~----l~fi~~VD~~dNELa~LE~IH~fVE~LDkyF-----------------ILDEmil~Gev~ETsk~~IL 72 (86)
.+.+++|+ ++|+++.|.++||++++|++|.||++|+.|| +||||+.+|.++||+++.|+
T Consensus 53 ~~~~~vy~~~~dl~~~~v~~~~eNel~~~e~l~~~v~~l~~~~~~v~e~~i~~N~~~v~~~LDEiid~G~i~etd~~~I~ 132 (141)
T PF01217_consen 53 DNYRIVYKRYSDLYFVVVGDENENELLLLEFLHRLVEVLDDYFGNVSEKDILENFDLVYLILDEIIDGGIILETDPNVIL 132 (141)
T ss_dssp TTEEEEEEEETTEEEEEEESSTSBHHHHHHHHHHHHHHHHHHHSS-SHHHHHHTHHHHHHHHHHHEETTEES--THHHHH
T ss_pred ccceeeeEeeccEEEEEEeecccchHHHHHHHHHhhhhhhhhhccccHHHHHHCHHHHHHHHHHHHhCCEEEECCHHHHH
Confidence 45799999 9999999999999999999999999999999 99999999999999999999
Q ss_pred ccchhcchh
Q 035597 73 TPDKTDGEN 81 (86)
Q Consensus 73 ~~i~~~~~~ 81 (86)
+++..++++
T Consensus 133 ~~v~~~~~~ 141 (141)
T PF01217_consen 133 KRVTMQDSA 141 (141)
T ss_dssp HHHHHCCC-
T ss_pred HHHHHhhcC
Confidence 999998864
No 6
>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.08 E-value=0.0012 Score=49.39 Aligned_cols=63 Identities=13% Similarity=0.109 Sum_probs=52.1
Q ss_pred CceeEEE----eeeEEEEcCCCchhhhHHHHHHHHHHhhhhh------------------hhheeecceeeeeechhhhc
Q 035597 15 PLKLHFE----FPRVVSMRTCGNKLAILKFIYLLVETADCGI------------------VIVEKVMDGCMAGTSKSNIL 72 (86)
Q Consensus 15 ~~~~~y~----l~fi~~VD~~dNELa~LE~IH~fVE~LDkyF------------------ILDEmil~Gev~ETsk~~IL 72 (86)
+.-++|+ ++|-+.--..||||........+-+.++--+ ++||++-||-++||..+.|.
T Consensus 61 g~~vvYk~~~Dl~fyv~G~~~ENEl~L~svL~~l~dal~llLr~nveKr~llEN~D~i~L~~DEiiD~GvILEtdp~~ia 140 (175)
T KOG3343|consen 61 GNTVVYKSVIDLHFYVVGSEEENELMLMSVLTCLFDALSLLLRKNVEKRELLENLDLIFLALDEIIDGGVILETDPNQIA 140 (175)
T ss_pred CcEEEEEecccEEEEEecCcchhHHHHHHHHHHHHHHHHHHHHhChhHHHHHhhhccceeehhhhccCceEEecCHHHHH
Confidence 3568899 7777777789999998888877776665555 99999999999999999999
Q ss_pred ccchh
Q 035597 73 TPDKT 77 (86)
Q Consensus 73 ~~i~~ 77 (86)
+++..
T Consensus 141 ~rv~~ 145 (175)
T KOG3343|consen 141 QRVAL 145 (175)
T ss_pred HHhcc
Confidence 88764
No 7
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=96.29 E-value=0.0037 Score=51.84 Aligned_cols=47 Identities=13% Similarity=0.042 Sum_probs=42.4
Q ss_pred eeeEEEEcCCCchhhhHHHHHHHHHHhhhhh-----------------hhheeecceeeeeech
Q 035597 22 FPRVVSMRTCGNKLAILKFIYLLVETADCGI-----------------VIVEKVMDGCMAGTSK 68 (86)
Q Consensus 22 l~fi~~VD~~dNELa~LE~IH~fVE~LDkyF-----------------ILDEmil~Gev~ETsk 68 (86)
.+||.++..+--.|.+.|+.|+.|.++-.|| +||||+-+|.-.-|..
T Consensus 65 i~~~~~st~e~pPL~~iefL~rv~dv~~eyFg~~s~~~Ik~N~~vv~ell~emiDnGfpl~tE~ 128 (418)
T KOG2740|consen 65 IFFCAVSTVETPPLMVIEFLHRVVDVLLEYFGGLSESKIKDNVVVVYELLDEMIDNGFPLVTEP 128 (418)
T ss_pred cEEEEEEeccCCChhHHHHHHHHHHHHHHHhcccCHhHhhcceeeHHHHHHHHHHcCCCcccCh
Confidence 8889998877779999999999999999999 9999999998766655
No 8
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=90.37 E-value=0.42 Score=40.00 Aligned_cols=56 Identities=16% Similarity=0.154 Sum_probs=51.0
Q ss_pred eeeEEEEcCCCchhhhHHHHHHHHHHhhhhh-----------------hhheeecceeeeeechhhhcccchh
Q 035597 22 FPRVVSMRTCGNKLAILKFIYLLVETADCGI-----------------VIVEKVMDGCMAGTSKSNILTPDKT 77 (86)
Q Consensus 22 l~fi~~VD~~dNELa~LE~IH~fVE~LDkyF-----------------ILDEmil~Gev~ETsk~~IL~~i~~ 77 (86)
++.+...-.+-|-.+++||..-.+.++..|| .||||+-.|..|.|+...+...+.+
T Consensus 62 l~lvaitksN~Nva~v~eFl~kl~avm~aYfgk~~Eeaiknnf~lI~ElLDemld~G~pqnte~~al~~~is~ 134 (446)
T KOG0938|consen 62 LWLVAITKSNANVAAVFEFLYKLDAVMNAYFGKDREEAIKNNFVLIYELLDEMLDFGIPQNTEPNALKAQISQ 134 (446)
T ss_pred EEEEEEecCCCchhhHHHHHHHHHHHHHHHhcccchhhhhhceEeHHHHHHHHHhcCCCccCChhHHHhhhhh
Confidence 8888888899999999999999999999999 8999999999999998887766654
No 9
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=88.08 E-value=0.65 Score=38.91 Aligned_cols=57 Identities=21% Similarity=0.189 Sum_probs=50.4
Q ss_pred eeeEEEEcCCCchhhhHHHHHHHHHHhhhhh-----------------hhheeecceeeeeechhhhcccchhcc
Q 035597 22 FPRVVSMRTCGNKLAILKFIYLLVETADCGI-----------------VIVEKVMDGCMAGTSKSNILTPDKTDG 79 (86)
Q Consensus 22 l~fi~~VD~~dNELa~LE~IH~fVE~LDkyF-----------------ILDEmil~Gev~ETsk~~IL~~i~~~~ 79 (86)
++++++.-.+.|-..+++++|.+++++-.|| .|||++-=|.. +|+..+|++..-++.
T Consensus 63 lylv~~~~~n~~a~~v~~~l~~~~~v~~~y~~~l~e~si~~n~vlvyElLde~mDFGyp-Q~t~s~iL~~yi~~~ 136 (424)
T KOG0937|consen 63 LYLVAGTRPNVSAALVLSFLYAVADVFGDYLSELEEESIRDNFVLVYELLDEVMDFGYP-QTTDSEILKNYITQK 136 (424)
T ss_pred eEEEEEeccCCCHHHHHHHHHHHHHHHHHHhccCCccceecchHHHHHHHHHHhccCCc-ccchHHHHHHHhccc
Confidence 9999999889999999999999999999999 89999999999 677777777665554
No 10
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=74.92 E-value=14 Score=27.91 Aligned_cols=65 Identities=9% Similarity=-0.018 Sum_probs=49.7
Q ss_pred EeeeccCCCCceeEEE----eeeEEEEcCCCchhhhHHHHHHHHHHhhhhh------------------hhheeecceee
Q 035597 6 LRVRVWSPKPLKLHFE----FPRVVSMRTCGNKLAILKFIYLLVETADCGI------------------VIVEKVMDGCM 63 (86)
Q Consensus 6 ~~~~~~~~~~~~~~y~----l~fi~~VD~~dNELa~LE~IH~fVE~LDkyF------------------ILDEmil~Gev 63 (86)
++..+-++.|--+++. ++|..+.|..||=+.+=-+.+.|+-.|-.+| ||+.++=.|++
T Consensus 94 l~~gd~f~~~k~vvW~~v~~l~ftLVce~hEN~lLa~~~L~~~~~~l~~~~~~l~~~~e~l~k~d~i~aiL~~fLP~GQL 173 (189)
T PF15001_consen 94 LPAGDPFSTPKIVVWLGVGSLCFTLVCEPHENRLLAENTLRLFIRHLLEHLKILSQPSEVLLKSDRILAILHRFLPHGQL 173 (189)
T ss_pred ccCCCCCCCCcEEEeeccCCEEEEEEecCchhHHHHHHHHHHHHHHHHHHHHHhCcHHHhhhhHHHHHHHHHHhCCCCcE
Confidence 3444444444455555 9999999999998888778888888887766 89999999998
Q ss_pred eeechhh
Q 035597 64 AGTSKSN 70 (86)
Q Consensus 64 ~ETsk~~ 70 (86)
.=.|.+-
T Consensus 174 LFlN~~~ 180 (189)
T PF15001_consen 174 LFLNHRF 180 (189)
T ss_pred EEEcHHH
Confidence 8887654
No 11
>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=61.42 E-value=23 Score=26.90 Aligned_cols=49 Identities=10% Similarity=0.017 Sum_probs=37.0
Q ss_pred cCCCchhhhHHHHHHHHHHhhhhh------------------hhheeecceeeeeechhhhcccchh
Q 035597 29 RTCGNKLAILKFIYLLVETADCGI------------------VIVEKVMDGCMAGTSKSNILTPDKT 77 (86)
Q Consensus 29 D~~dNELa~LE~IH~fVE~LDkyF------------------ILDEmil~Gev~ETsk~~IL~~i~~ 77 (86)
--++||...-+-...+--.|+-.| +.||.|-+|-|.||..+.|..++..
T Consensus 86 ~meeNE~~l~q~f~~ir~Al~li~k~~~dkr~v~enYDqivl~vdEtid~Gvilet~s~~ia~rv~K 152 (187)
T COG5541 86 PMEENEPFLGQVFDEIRAALILIVKTPTDKRNVWENYDQIVLLVDETIDEGVILETKSDEIADRVPK 152 (187)
T ss_pred ccccccHHHHHHHHHHHHHHHHHHcCCcchhhHHhhhceEEEeeehhcccceEeecChHHHHHhCCC
Confidence 345777766655555555555544 8899999999999999999998864
No 12
>PF00780 CNH: CNH domain; InterPro: IPR001180 Based on sequence similarities a domain of homology has been identified in the following proteins []: Citron and Citron kinase. These two proteins interact with the GTP-bound forms of the small GTPases Rho and Rac but not with Cdc42. Myotonic dystrophy kinase-related Cdc42-binding kinase (MRCKalpha). This serine/threonine kinase interacts with the GTP-bound form of the small GTPase Cdc42 and to a lesser extent with that of Rac. NCK Interacting Kinase (NIK), a serine/threonine protein kinase. ROM-1 and ROM-2, from yeast. These proteins are GDP/GTP exchange proteins (GEPs) for the small GTP binding protein Rho1. This domain, called the citron homology domain, is often found after cysteine rich and pleckstrin homology (PH) domains at the C-terminal end of the proteins []. It acts as a regulatory domain and could be involved in macromolecular interactions [, ].; GO: 0005083 small GTPase regulator activity
Probab=38.16 E-value=34 Score=24.49 Aligned_cols=21 Identities=19% Similarity=0.623 Sum_probs=19.4
Q ss_pred ccCCCCceeEEEeeeEEEEcC
Q 035597 10 VWSPKPLKLHFEFPRVVSMRT 30 (86)
Q Consensus 10 ~~~~~~~~~~y~l~fi~~VD~ 30 (86)
.|+.+|..+.|.-|+++++..
T Consensus 226 ~W~~~p~~~~~~~pyli~~~~ 246 (275)
T PF00780_consen 226 QWSSAPQSVAYSSPYLIAFSS 246 (275)
T ss_pred EcCCchhEEEEECCEEEEECC
Confidence 699999999999999999875
No 13
>COG1993 PII-like signaling protein [Signal transduction mechanisms]
Probab=34.85 E-value=22 Score=24.97 Aligned_cols=41 Identities=20% Similarity=0.323 Sum_probs=29.2
Q ss_pred ccCCCCceeEEEeeeEE-EEcCCCchhhhHHHHHHHHHHhhhhhhhheeecceee
Q 035597 10 VWSPKPLKLHFEFPRVV-SMRTCGNKLAILKFIYLLVETADCGIVIVEKVMDGCM 63 (86)
Q Consensus 10 ~~~~~~~~~~y~l~fi~-~VD~~dNELa~LE~IH~fVE~LDkyFILDEmil~Gev 63 (86)
-++.+..|+.++||.++ +||..+| |-+|++. +||++-+|.+
T Consensus 55 ~h~~~if~Ls~~LPVviEvVD~eek-------I~~~l~~------l~e~~~~~li 96 (109)
T COG1993 55 IHGSKIFRLSTDLPVVVEVVDEEEK-------IERFLPE------LDEIIKNGLI 96 (109)
T ss_pred ccccchhhccCCCCEEEEEeCCHHH-------HHHHHHH------HHHHhhcceE
Confidence 46778889999999876 5677666 6666664 5677777733
No 14
>PF11447 DUF3201: Protein of unknown function (DUF3201); InterPro: IPR024505 This archaeal family of proteins has no known function.; PDB: 1YB3_A.
Probab=32.81 E-value=28 Score=25.77 Aligned_cols=57 Identities=11% Similarity=0.048 Sum_probs=36.1
Q ss_pred eeeEEEEcCCCchhhhHHHHHHHHHHhhhhh------hhheeecceeeeeechhhhcccchhcchhhh
Q 035597 22 FPRVVSMRTCGNKLAILKFIYLLVETADCGI------VIVEKVMDGCMAGTSKSNILTPDKTDGENIL 83 (86)
Q Consensus 22 l~fi~~VD~~dNELa~LE~IH~fVE~LDkyF------ILDEmil~Gev~ETsk~~IL~~i~~~~~~~~ 83 (86)
+||++++.... ...|++-.|++..-|.| -|.-+.- +---.|.++|.++|..++|.+.
T Consensus 68 ~YFvfav~kE~---is~~Fv~~fl~~F~ksfIYG~ENFLeDfYN--~~~p~~~~Ev~~~I~~S~Ee~~ 130 (150)
T PF11447_consen 68 FYFVFAVPKEK---ISEEFVKEFLRKFPKSFIYGSENFLEDFYN--RDNPRSPDEVWKKIKRSDEEVI 130 (150)
T ss_dssp EEEEEEEEGGG-----HHHHHHHHHH-SEEEEESS-TTT-EEEE--TTS---HHHHHHHHHTSS-SEE
T ss_pred EEEEEEeeHHH---hhHHHHHHHHHhCchhhhhhHHHHHHHHhc--ccCCCCHHHHHHHHHhchhhhe
Confidence 89999999765 78999999999999988 3443333 1111233478888888877654
No 15
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.69 E-value=1.2e+02 Score=26.42 Aligned_cols=49 Identities=16% Similarity=0.099 Sum_probs=40.7
Q ss_pred CCCceeEEE----eeeEEEEcCCCchhhhHHHHHHHHHHhhhhh-----------------hhheeecce
Q 035597 13 PKPLKLHFE----FPRVVSMRTCGNKLAILKFIYLLVETADCGI-----------------VIVEKVMDG 61 (86)
Q Consensus 13 ~~~~~~~y~----l~fi~~VD~~dNELa~LE~IH~fVE~LDkyF-----------------ILDEmil~G 61 (86)
+.+.|-||+ +|.++....+-|-|.-|+..++|..+.-.|- -.||++-=|
T Consensus 51 t~~VRYVYqP~d~lY~vLITtk~SNIleDl~TL~Lfskvipey~~slde~eI~~~~FelifAFDEivsLG 120 (512)
T KOG2635|consen 51 TDSVRYVYQPLDNLYIVLITTKQSNILEDLETLRLFSKVIPEYCSSLDEKEILENAFELIFAFDEIVSLG 120 (512)
T ss_pred cccEEEEEEecccEEEEEEeccccchhhHHHHHHHHHHhchhhhhhhhHHHHHHhhhhhhhccchhhhhc
Confidence 456789999 9999999999999999999999986555543 778988888
No 16
>PF01172 SBDS: Shwachman-Bodian-Diamond syndrome (SBDS) protein ; InterPro: IPR019783 This entry represents the N-terminal domain of proteins that are highly conserved in species ranging from archaea to vertebrates and plants []. The family contains several Shwachman-Bodian-Diamond syndrome (SBDS, OMIM 260400) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. It is characterised by bone marrow failure and leukemia predisposition. Members of this family play a role in RNA metabolism [, ]. In yeast Sdo1 is involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes. Together with the EF-2-like GTPase RIA1 (EfI1), it triggers the GTP-dependent release of TIF6 from 60S pre-ribosomes in the cytoplasm, thereby activating ribosomes for translation competence by allowing 80S ribosome assembly and facilitating TIF6 recycling to the nucleus, where it is required for 60S rRNA processing and nuclear export. This data links defective late 60S subunit maturation to an inherited bone marrow failure syndrome associated with leukemia predisposition []. A number of uncharacterised hydrophilic proteins of about 30 kDa share regions of similarity. These include, Mouse protein 22A3. Saccharomyces cerevisiae chromosome XII hypothetical protein YLR022c. Caenorhabditis elegans hypothetical protein W06E11.4. Methanocaldococcus jannaschii (Methanococcus jannaschii) hypothetical protein MJ0592. ; PDB: 1NYN_A 2WBM_B 1P9Q_C 1T95_A 2KDO_A 2L9N_A.
Probab=24.17 E-value=26 Score=22.98 Aligned_cols=17 Identities=18% Similarity=0.235 Sum_probs=12.7
Q ss_pred hhheeecceeeeeechh
Q 035597 53 VIVEKVMDGCMAGTSKS 69 (86)
Q Consensus 53 ILDEmil~Gev~ETsk~ 69 (86)
|+.+++..|++|.|..+
T Consensus 71 ii~~IL~~Ge~q~t~~~ 87 (91)
T PF01172_consen 71 IIKKILKKGEIQLTAEE 87 (91)
T ss_dssp HHHHHHHHSEEE--HHH
T ss_pred HHHHHHhcCCccCChhh
Confidence 88889999999988764
No 17
>PF11453 DUF2950: Protein of unknown function (DUF2950); InterPro: IPR021556 This is a bacterial family of uncharacterised proteins.
Probab=23.93 E-value=61 Score=25.94 Aligned_cols=23 Identities=17% Similarity=0.134 Sum_probs=21.3
Q ss_pred CCCchhhhHHHHHHHHHHhhhhh
Q 035597 30 TCGNKLAILKFIYLLVETADCGI 52 (86)
Q Consensus 30 ~~dNELa~LE~IH~fVE~LDkyF 52 (86)
...|||++.+..|.||+.-..|.
T Consensus 107 IGRNEL~aI~~~~ayvdAQ~eYa 129 (271)
T PF11453_consen 107 IGRNELAAIQTLLAYVDAQREYA 129 (271)
T ss_pred cchhHHHHHHHHHHHHHHHHHHH
Confidence 46799999999999999999998
No 18
>TIGR03358 VI_chp_5 type VI secretion protein, VC_A0107 family. Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (PubMed:16763151). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al.
Probab=21.61 E-value=92 Score=22.90 Aligned_cols=17 Identities=18% Similarity=0.540 Sum_probs=14.6
Q ss_pred CCCCceeEEE-----------eeeEEEE
Q 035597 12 SPKPLKLHFE-----------FPRVVSM 28 (86)
Q Consensus 12 ~~~~~~~~y~-----------l~fi~~V 28 (86)
+++-.+|+|+ |||.++|
T Consensus 7 pk~RV~I~Y~~etgga~~~vELPf~~~V 34 (159)
T TIGR03358 7 RKPRVQITYDVETGGAEEKVELPLVVGV 34 (159)
T ss_pred CCCceeEEEEccCCCceeeeecCeEEEE
Confidence 4567899999 9999998
No 19
>cd09030 DUF1425 Putative periplasmic lipoprotein. This bacterial family of proteins contains members described as putative lipoproteins, some are also known as YcfL. The function of this family is unknown. Family members have also been annotated as predicted periplasmic lipoproteins (COG5633), and appear to contain an N-terminal membrane lipoprotein lipid attachment side (pfam08139), which is not included in this alignment model.
Probab=21.30 E-value=1.3e+02 Score=19.44 Aligned_cols=18 Identities=33% Similarity=0.469 Sum_probs=13.5
Q ss_pred eeccCCCCceeEEEeeeE
Q 035597 8 VRVWSPKPLKLHFEFPRV 25 (86)
Q Consensus 8 ~~~~~~~~~~~~y~l~fi 25 (86)
.+.-++.|.+++|||+..
T Consensus 40 l~N~~~~~~~l~Yrf~Wy 57 (101)
T cd09030 40 LSNTSSKPLTLQYRFYWY 57 (101)
T ss_pred EEeCCCCCEEEEEEEEEE
Confidence 345567899999997763
Done!