Query 042402
Match_columns 523
No_of_seqs 148 out of 848
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 05:54:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042402.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042402hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2635 Medium subunit of clat 100.0 1.1E-96 2E-101 741.6 45.9 499 1-523 1-512 (512)
2 KOG0938 Adaptor complexes medi 100.0 5E-81 1.1E-85 609.9 36.7 400 3-522 2-445 (446)
3 KOG0937 Adaptor complexes medi 100.0 2.6E-68 5.6E-73 543.7 35.4 391 4-522 2-422 (424)
4 KOG2740 Clathrin-associated pr 100.0 2.2E-58 4.8E-63 455.4 33.6 402 2-522 1-416 (418)
5 PF00928 Adap_comp_sub: Adapto 100.0 6.4E-46 1.4E-50 371.7 25.6 235 285-522 9-260 (262)
6 PF01217 Clat_adaptor_s: Clath 99.9 1.5E-24 3.3E-29 197.5 16.7 136 2-137 1-138 (141)
7 KOG2677 Stoned B synaptic vesi 99.8 5.5E-21 1.2E-25 200.7 5.1 235 284-520 582-892 (922)
8 COG5030 APS2 Clathrin adaptor 99.8 2E-19 4.2E-24 156.7 12.6 129 3-131 2-132 (152)
9 KOG0935 Clathrin adaptor compl 99.7 4.1E-17 9E-22 138.5 10.6 133 3-135 2-137 (143)
10 KOG0934 Clathrin adaptor compl 99.7 2.2E-17 4.8E-22 143.8 7.1 124 3-129 2-130 (145)
11 KOG0936 Clathrin adaptor compl 99.5 1.2E-13 2.7E-18 122.2 11.8 134 2-135 1-142 (182)
12 PF10291 muHD: Muniscin C-term 99.2 5.8E-09 1.3E-13 104.3 21.8 226 290-521 2-255 (257)
13 KOG3343 Vesicle coat complex C 98.7 1.3E-07 2.8E-12 85.1 12.1 140 2-143 8-152 (175)
14 COG5541 RET3 Vesicle coat comp 97.2 0.00095 2.1E-08 60.2 6.9 135 2-136 7-152 (187)
15 PF03164 Mon1: Trafficking pro 92.0 1.4 3E-05 47.4 11.4 80 5-87 13-96 (415)
16 PF08923 MAPKK1_Int: Mitogen-a 91.3 2.1 4.6E-05 37.8 9.9 91 3-93 17-115 (119)
17 PF04099 Sybindin: Sybindin-li 87.5 6.6 0.00014 35.7 10.4 91 3-94 1-115 (142)
18 PF13774 Longin: Regulated-SNA 86.1 4.8 0.00011 32.7 8.0 50 46-95 16-65 (83)
19 COG5122 TRS23 Transport protei 80.9 14 0.00029 32.2 8.6 91 1-94 1-106 (134)
20 PF15001 AP-5_subunit_s1: AP-5 79.2 13 0.00029 35.4 9.0 78 54-131 104-182 (189)
21 KOG3368 Transport protein part 72.8 28 0.00061 31.2 8.6 86 1-88 1-102 (140)
22 KOG0997 Uncharacterized conser 70.1 29 0.00062 37.7 9.5 82 6-91 120-207 (523)
23 KOG3369 Transport protein part 70.1 46 0.001 31.3 9.7 45 48-94 125-170 (199)
24 KOG0861 SNARE protein YKT6, sy 63.8 31 0.00067 32.5 7.3 91 1-94 1-102 (198)
25 PF03504 Chlam_OMP6: Chlamydia 63.2 27 0.00059 28.7 6.0 42 413-458 42-83 (95)
26 PF00235 Profilin: Profilin; 61.2 70 0.0015 27.7 9.0 86 3-90 16-121 (121)
27 PF09201 SRX: SRX; InterPro: 52.3 34 0.00074 31.0 5.3 67 4-72 3-86 (148)
28 KOG2265 Nuclear distribution p 32.7 49 0.0011 31.2 3.4 41 414-454 26-84 (179)
29 KOG0592 3-phosphoinositide-dep 32.4 1.7E+02 0.0037 32.6 7.9 65 45-122 132-196 (604)
30 KOG0859 Synaptobrevin/VAMP-lik 31.9 4.8E+02 0.01 25.3 12.1 91 1-97 1-94 (217)
31 KOG0862 Synaptobrevin/VAMP-lik 30.6 3.2E+02 0.0069 26.8 8.6 50 48-97 53-102 (216)
32 KOG0781 Signal recognition par 28.5 4.3E+02 0.0094 29.2 10.0 108 5-119 4-116 (587)
33 PF08784 RPA_C: Replication pr 28.4 85 0.0018 26.4 4.0 16 110-125 83-98 (102)
34 PF03259 Robl_LC7: Roadblock/L 27.4 2.3E+02 0.005 22.5 6.4 66 3-68 15-89 (91)
35 KOG0582 Ste20-like serine/thre 23.3 8.3E+02 0.018 26.9 10.9 100 6-122 44-148 (516)
36 PF04086 SRP-alpha_N: Signal r 22.4 1.2E+02 0.0027 30.4 4.6 51 45-95 18-70 (279)
No 1
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.1e-96 Score=741.63 Aligned_cols=499 Identities=50% Similarity=0.820 Sum_probs=434.9
Q ss_pred CeEEEEEEEcCCCCEEEEEcceecchHHHHHHHhhhchhhcCCCCCcEEEeCCEEEEEEEcCCEEEEEEEcCCCCHHHHH
Q 042402 1 MVVLAASIVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGTGKQHTYVETENVRYVYQPIEALYLLLVTNKQSNILEDL 80 (523)
Q Consensus 1 m~v~s~~Il~~~G~~lisR~yr~~~r~~~e~~l~~F~~~i~~~~~~p~i~~~~~~yvy~~~~~ly~v~~t~~n~n~~~~l 80 (523)
|||++|+|++++|+.+|+||||+|+|.++|++|++|++++..+++|+++|.+.+||||++.++||+|++|++++|++++|
T Consensus 1 Mvvlaa~i~t~~Gk~ivsRqf~~Msr~RIEgLl~aFpkLv~~~~qhT~vEt~~VRYVYqP~d~lY~vLITtk~SNIleDl 80 (512)
T KOG2635|consen 1 MVVLAASINTKTGKAIVSRQFREMSRSRIEGLLAAFPKLVSAGKQHTFVETDSVRYVYQPLDNLYIVLITTKQSNILEDL 80 (512)
T ss_pred CeEEEEEEeecCCceeeehHhHhhhHHHHHHHHHHhHHhhccCCCccEEecccEEEEEEecccEEEEEEeccccchhhHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhcCCCChhhHHhhHHHHHHhHHhHHhCCeecccCHHHHHHHhhccchHHHHHHHHhhhcchhhhHHHH
Q 042402 81 ETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLGHKENVTVAQVKQYCEMESHEEKLHKLVVQSKINETKDVMK 160 (523)
Q Consensus 81 e~L~~l~~il~~y~g~l~E~~I~~niyel~~~lDEiid~G~pq~t~~~~lk~~i~m~s~ee~i~~~~~~~ke~eak~~~k 160 (523)
++|++|.+++..||..++|+.|.+|+|||+|+|||++..||.++.++.|||+|++|||||||+|++++++||.||+++||
T Consensus 81 ~TL~Lfskvipey~~slde~eI~~~~FelifAFDEivsLGyre~v~laQikty~eMdSHEEKi~e~v~~nke~ea~q~mk 160 (512)
T KOG2635|consen 81 ETLRLFSKVIPEYCSSLDEKEILENAFELIFAFDEIVSLGYRENVNLAQIKTYLEMDSHEEKIHELVMRNKEREAKQEMK 160 (512)
T ss_pred HHHHHHHHhchhhhhhhhHHHHHHhhhhhhhccchhhhhcccccccHHHhhhhhccccHHHHHHHHHHHhhhHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhhhhhhhccCCC---CCccccccCCCCccccccccccccCCCCCCCCCCCcccccccccccccCCCCCC-CCCC
Q 042402 161 RKASEIDKSKIEKNRGDK---GGFMSLQSMGSGRIESSFSDMSISSGGGGFGSGSGFGLATTDVETFSSKSKGRP-PSSA 236 (523)
Q Consensus 161 ~~a~e~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~s~~~~~~~~p-~~~~ 236 (523)
||||||+++|.+..+++. ++|...|++|-...+ .+.+....++...+.+..+ ...+
T Consensus 161 rKaKElqr~r~ea~rrgg~~~~~~~~~~s~g~~~~s--------------------~~~~~~~~~~~~~~~~~~sa~~~~ 220 (512)
T KOG2635|consen 161 RKAKELQRARKEAERRGGSLNPGFDAIGSSGYSSVS--------------------TTNAINRVESIAQKPKQQSAAKAS 220 (512)
T ss_pred HHHHHHHHHHHhhhccccccCCCccccccccccCCc--------------------ccchhhccccccccccccccccCC
Confidence 999999999999877651 233222221110000 0011111111111111111 1222
Q ss_pred CCCCCCcCccccccCCc-hhhhhhhhhccceeecccCccc-c--ccccccCCCCCCCCeEEEEEEEEEEEEecCCCeEEE
Q 042402 237 NAPPKGLGMQLGKSQRT-NQFLESLKAEGEVILEDVKPIA-G--QSRAAAAAPPLTDPITLTVEEKINVSLKRDGGMSNF 312 (523)
Q Consensus 237 ~~~~~~~gm~lgk~~~~-n~~~~~l~~e~~~~~~~~~~~~-~--~~~~~~~~~~~~neI~vdV~Ekv~~~~~~~G~v~~~ 312 (523)
++| .+||+|||+.+. +.++++|++||+.+...+.+.. + .+++.+......|.||+.++|+|++.++|||.+.+.
T Consensus 221 s~p--ak~mklG~k~~~s~~~~d~Lk~ege~ia~~~s~~g~~s~aap~~~~p~v~~e~v~i~ieEkln~~~~RDGgi~s~ 298 (512)
T KOG2635|consen 221 SAP--AKAMKLGKKTKNSDTFVDKLKGEGERIAGASSAIGSASSAAPPPTAPDVPEESVHIVIEEKLNVRLSRDGGIKSG 298 (512)
T ss_pred CCC--chhhhhcccccchhhHHHHhhccccccccccccccccccCCCCCCCCCCccceEEEEEeeeEeEEEcccCCccce
Confidence 334 569999976655 4899999999998765422211 1 111122235667779999999999999999999999
Q ss_pred EEEEEEEEEEecCCCceEEEEeeCCCCCCCCcccccccCcccccccceEEEeCCCCCcccccc-----ccccCCCCCcCC
Q 042402 313 DVQGTLSLQILNQEDGLIQVQIETGGNPGILFKTHPNMNKELFTHENILGLKDPNRPFPQAKL-----WRMQSADESMVP 387 (523)
Q Consensus 313 eV~G~i~~~~~lsg~p~~~l~ln~~~~~~~d~~fHpcVd~~~f~~~r~Isf~pPdg~F~L~~~-----yr~~~~d~~~lP 387 (523)
|++|.|.+++.+..+.++.|.|.+...++.++++||++||+.|.+.++|.+++|+++||+++. ||....|+..+|
T Consensus 299 E~qG~lsLrI~d~e~~~i~lkl~n~~~~g~q~ktHPNlDK~~f~s~s~iglk~~~K~FPvn~~VGvLkWR~~~~des~iP 378 (512)
T KOG2635|consen 299 EVQGTLSLRIKDEEYGDIELKLANGRDKGTQLKTHPNLDKKVFLSSSLIGLKRPEKPFPVNSDVGVLKWRMVDEDESEIP 378 (512)
T ss_pred eeeeeEEEEEccccccceEEEEcCCCCcceeeeeCCCcchhhhccccccccccCCCCCCcCCcceEEEEeecccccccCc
Confidence 999999999999999999999998777889999999999999999999999999999999954 999998999999
Q ss_pred eEEEEEEEeeCCeEEEEEEEEecCCceeeeEEEEecCCCCCCCCeEEeecceEEEECCCCEEEEEEceecCCCceEEEEE
Q 042402 388 LTINCWPSVSGNETYVSIEYEASTMFDLRNVVISVPLPALREAPSVRQIDGEWRYDSRNSVLEWTILLIDNSNRSGSMEF 467 (523)
Q Consensus 388 ~~i~~~~~~~~~~~~v~i~~~~~~~~~~~~V~V~iPlP~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~i~~~~~s~s~ef 467 (523)
|+++|||++++..+.|+|||++.....++||.|.||+|.+. .|++..++|+|.|++.++.+.|+|+.| .+|.+|++||
T Consensus 379 lTincWPSes~~g~dV~iEYe~~~~~eL~dV~i~iPlP~~i-apsv~~~Dge~~~~~~~~~leW~I~~I-a~N~SGslEF 456 (512)
T KOG2635|consen 379 LTINCWPSESGNGYDVNIEYEAVLECELNDVIITIPLPANI-APSVGECDGEYRYDERKNVLEWSIGVI-AKNFSGSLEF 456 (512)
T ss_pred eEEEeccccCCCCeEEEEEEeehhcccccceEEEeeccccc-CCccceecceEEeccccceeEEEeeee-ccCCCCcEEE
Confidence 99999999999889999999997778899999999999977 899999999999999999999999999 6789999999
Q ss_pred EeCCCCCCCCCCeEEEEEecccccCceEeEEEECCCCCCCeeeEEEEEEeeceEEC
Q 042402 468 VVPPADSSSFFPISVRFSATSTYSDLKVVNIIPLRGGAPPKFSQRTVLITENYQVV 523 (523)
Q Consensus 468 ~~~~~~~~~~~Pi~v~F~ip~t~Sgl~V~~l~i~~~~~~i~~~~~~~~~~~~y~i~ 523 (523)
+|++.+++.|||++|.|....+++||.|..|...+++++++|++++.|.+|+|+|+
T Consensus 457 s~~~~~~~~fFPl~VsF~s~~~ftgl~vqkVv~~~~~~~~~y~~~t~f~~dky~Vv 512 (512)
T KOG2635|consen 457 SCPASDPDGFFPLSVSFTSDTVFTGLFVQKVVRNDGHAPVRYSVETTFEVDKYEVV 512 (512)
T ss_pred eecCCCCCceeeEEEEEEecccccceEEEEEEEcCCCCCceeEEEEEEEeeeeEeC
Confidence 99999999999999999999999999999998888889999999999999999996
No 2
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=5e-81 Score=609.93 Aligned_cols=400 Identities=19% Similarity=0.257 Sum_probs=344.7
Q ss_pred EEEEEEEcCCCCEEEEEcce-ecchHHHHHHHhhhchhhcC--CCCCcEEEeCCEEEEEEEcCCEEEEEEEcCCCCHHHH
Q 042402 3 VLAASIVSKSGKILVSRQFV-DMSRIRIEGLLAAFPKLVGT--GKQHTYVETENVRYVYQPIEALYLLLVTNKQSNILED 79 (523)
Q Consensus 3 v~s~~Il~~~G~~lisR~yr-~~~r~~~e~~l~~F~~~i~~--~~~~p~i~~~~~~yvy~~~~~ly~v~~t~~n~n~~~~ 79 (523)
|.++||+|.+|++||.|.|| |+.|+..|. |+-.+.+ ...||+..+++.+|+|.++++||+|++|+.|.|.+.+
T Consensus 2 isglfi~n~rGevlink~fr~dlkrs~~di----FRv~vi~n~d~r~PV~~igsttf~~~r~~nl~lvaitksN~Nva~v 77 (446)
T KOG0938|consen 2 ISGLFIYNLRGEVLINKTFRDDLKRSIVDI----FRVQVINNLDVRSPVLTIGSTTFHHIRSSNLWLVAITKSNANVAAV 77 (446)
T ss_pred cceEEEEeccCcEEEehhhhhhhhhhHHHH----HHHhhhhccccCCCeeEecceeEEEEeeccEEEEEEecCCCchhhH
Confidence 57899999999999999999 999998888 9988887 3478999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhcCCCChhhHHhh---HHHHHHhHHhHHhCCeecccCHHHHHHHhhccchHHHHHHHHhhhcchhhh
Q 042402 80 LETLRLLSKLVPEYSYSLDEEGICKT---AFELLFAFDEVISLGHKENVTVAQVKQYCEMESHEEKLHKLVVQSKINETK 156 (523)
Q Consensus 80 le~L~~l~~il~~y~g~l~E~~I~~n---iyel~~~lDEiid~G~pq~t~~~~lk~~i~m~s~ee~i~~~~~~~ke~eak 156 (523)
+|||..+.+++..|||.++|+.|++| |||| ||||+||||||+|++++|+.+|..+ .+.
T Consensus 78 ~eFl~kl~avm~aYfgk~~Eeaiknnf~lI~El---LDemld~G~pqnte~~al~~~is~~----~Vr------------ 138 (446)
T KOG0938|consen 78 FEFLYKLDAVMNAYFGKDREEAIKNNFVLIYEL---LDEMLDFGIPQNTEPNALKAQISQK----GVR------------ 138 (446)
T ss_pred HHHHHHHHHHHHHHhcccchhhhhhceEeHHHH---HHHHHhcCCCccCChhHHHhhhhhh----hhh------------
Confidence 99999999999999999999999999 9999 9999999999999999999999862 210
Q ss_pred HHHHhhhhhhhhhhhhhccCCCCCccccccCCCCccccccccccccCCCCCCCCCCCcccccccccccccCCCCCCCC-C
Q 042402 157 DVMKRKASEIDKSKIEKNRGDKGGFMSLQSMGSGRIESSFSDMSISSGGGGFGSGSGFGLATTDVETFSSKSKGRPPS-S 235 (523)
Q Consensus 157 ~~~k~~a~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~s~~~~~~~~p~~-~ 235 (523)
..++..+. .. ++.+. +... ++++ .
T Consensus 139 --------------------s~g~~ls~---------k~-------s~~sq---------~~~~----------~ssqv~ 163 (446)
T KOG0938|consen 139 --------------------SMGGVLSS---------KS-------SPTSQ---------ATEL----------RSSQVT 163 (446)
T ss_pred --------------------ccccccCC---------cC-------CCCcc---------cccc----------cccccc
Confidence 00111110 00 00000 0000 1111 1
Q ss_pred CCCCCCCcCccccccCCchhhhhhhhhccceeecccCccccccccccCCCCCCCCeEEEEEEEEEEEEecCCCeEEEEEE
Q 042402 236 ANAPPKGLGMQLGKSQRTNQFLESLKAEGEVILEDVKPIAGQSRAAAAAPPLTDPITLTVEEKINVSLKRDGGMSNFDVQ 315 (523)
Q Consensus 236 ~~~~~~~~gm~lgk~~~~n~~~~~l~~e~~~~~~~~~~~~~~~~~~~~~~~~~neI~vdV~Ekv~~~~~~~G~v~~~eV~ 315 (523)
-..+||++|++ |.+||||+||.|++|++|+++|.|++++|.
T Consensus 164 G~i~WRr~Gi~---------------------------------------ykknevfldvvErvNlLmS~~GnVLrs~Vs 204 (446)
T KOG0938|consen 164 GKIGWRREGIK---------------------------------------YKKNEVFLDVVERVNLLMSSDGNVLRSDVS 204 (446)
T ss_pred cccccccccce---------------------------------------eccceeEeEehheeeeEEcCCCCEEEeecc
Confidence 14479999983 344599999999999999999999999999
Q ss_pred EEEEEEEecCCCceEEEEeeCCC----------------------CC----CCCcccccccCcccccccceEEEeCCCCC
Q 042402 316 GTLSLQILNQEDGLIQVQIETGG----------------------NP----GILFKTHPNMNKELFTHENILGLKDPNRP 369 (523)
Q Consensus 316 G~i~~~~~lsg~p~~~l~ln~~~----------------------~~----~~d~~fHpcVd~~~f~~~r~Isf~pPdg~ 369 (523)
|.+.|+++|||||+|+++|||.- ++ .+||+||+||++++|+++++|+|+||||+
T Consensus 205 G~V~mk~~LSGmPeckfGlNDkl~~e~kq~esks~~~n~~~~sks~~g~v~leDc~FHqCV~L~kFn~eh~IsFvPPDGe 284 (446)
T KOG0938|consen 205 GTVDMKTHLSGMPECKFGLNDKLGMESKQSESKSDFGNKNFPSKSGKGSVLLEDCTFHQCVRLDKFNSEHIISFVPPDGE 284 (446)
T ss_pred cEEEEEEeccCCcccccccCcccceeeccccccccccccCCCcccCCceEEeeccchheeeccccccccceEEEeCCCCc
Confidence 99999999999999999999850 01 28999999999999999999999999999
Q ss_pred ccccccccccCCCCCcCCeEEEEEEEeeCC---eEEEEEEEEecCCceeeeEEEEecCCCCCCCCeEEeecceEEEECCC
Q 042402 370 FPQAKLWRMQSADESMVPLTINCWPSVSGN---ETYVSIEYEASTMFDLRNVVISVPLPALREAPSVRQIDGEWRYDSRN 446 (523)
Q Consensus 370 F~L~~~yr~~~~d~~~lP~~i~~~~~~~~~---~~~v~i~~~~~~~~~~~~V~V~iPlP~~~~~~~~~~~~G~~~~~~~~ 446 (523)
|+|| .||.+. +..|||+|.|.+++.+. ++.|+|++.|++.+.+.+|.++||+|+++..+.+....|++.|.|++
T Consensus 285 ~ELM-kYr~~e--nInlPFrV~PiV~el~r~kie~ri~iks~f~~kl~a~~v~~rIPvP~ntv~~n~~v~~Gkaky~pse 361 (446)
T KOG0938|consen 285 FELM-KYRVTE--NINLPFRVTPIVTELGRTKIEYRITIKSLFPPKLLAKDVVVRIPVPPNTVKCNISVSNGKAKYVPSE 361 (446)
T ss_pred eEeE-eeeecc--CcccceEeeeheecccceeEEEEEEEeccCCchhhhcceEEEecCCCccccceeEEecCccccCccc
Confidence 9999 799876 78999999999999875 78899999999999999999999999999999999999999999999
Q ss_pred CEEEEEEceecC-CCceEEEEEEeCC----CCCCCCCCeEEEEEecc-cccCceEeEEEECCCCCCCee--eEEEEEEee
Q 042402 447 SVLEWTILLIDN-SNRSGSMEFVVPP----ADSSSFFPISVRFSATS-TYSDLKVVNIIPLRGGAPPKF--SQRTVLITE 518 (523)
Q Consensus 447 ~~l~W~I~~i~~-~~~s~s~ef~~~~----~~~~~~~Pi~v~F~ip~-t~Sgl~V~~l~i~~~~~~i~~--~~~~~~~~~ 518 (523)
++++|+|+++.| +|.+.++|+++.. ...|..+||+++|++|| +.|||.|+||++.+.++..+- +.++..+++
T Consensus 362 n~ivWki~kf~G~tE~tlsAevels~Tt~nkq~WtrPPIsleFeV~MFt~SGL~VrylkV~e~~Sk~~~vkWVrYitkaG 441 (446)
T KOG0938|consen 362 NAIVWKINKFNGLTESTLSAEVELSDTTQNKQQWTRPPISLEFEVPMFTNSGLVVRYLKVSEKDSKHRAVKWVRYITKAG 441 (446)
T ss_pred ceEEEEecccCCcccceeEEEEEeccCccccccccCCCceeEEeeeeecCCceEEEEEEEecccCCCceEEEEEEecccc
Confidence 999999999999 8888999988852 34588999999999999 999999999999995433322 589999999
Q ss_pred ceEE
Q 042402 519 NYQV 522 (523)
Q Consensus 519 ~y~i 522 (523)
+|+|
T Consensus 442 syEi 445 (446)
T KOG0938|consen 442 SYEI 445 (446)
T ss_pred eeee
Confidence 9998
No 3
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.6e-68 Score=543.66 Aligned_cols=391 Identities=19% Similarity=0.267 Sum_probs=329.0
Q ss_pred EEEEEEcCCCCEEEEEcce-ecchHHHHHHH-hhhchhhcCCCCCcEEEeCCEEEEEEEcCCEEEEEEEcCCCCHHHHHH
Q 042402 4 LAASIVSKSGKILVSRQFV-DMSRIRIEGLL-AAFPKLVGTGKQHTYVETENVRYVYQPIEALYLLLVTNKQSNILEDLE 81 (523)
Q Consensus 4 ~s~~Il~~~G~~lisR~yr-~~~r~~~e~~l-~~F~~~i~~~~~~p~i~~~~~~yvy~~~~~ly~v~~t~~n~n~~~~le 81 (523)
.|+||+|.+|++|++|.|| +++.+.++.++ ..|.+. .....+|++..++.+|+|.++++||++++++.|.|+..+++
T Consensus 2 sa~fild~~G~~lisr~yr~dv~~s~~~~F~~~l~~~e-~~~~~~p~l~~~g~~~~~ik~s~lylv~~~~~n~~a~~v~~ 80 (424)
T KOG0937|consen 2 SAVFILDHKGEVLISRDYRGDVPMSSTEKFFRKLFEKE-EGDESPPFLVHDGSRFIHIKHSNLYLVAGTRPNVSAALVLS 80 (424)
T ss_pred ceEEEEcCCCcEeEeecccccCChhhhhhHHHHHhhhc-ccCCCCCeEEeCCceEEEEeecceEEEEEeccCCCHHHHHH
Confidence 5899999999999999999 99999999843 222222 22456899999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhcCCCChhhHHhh---HHHHHHhHHhHHhCCeecccCHHHHHHHhhccchHHHHHHHHhhhcchhhhHH
Q 042402 82 TLRLLSKLVPEYSYSLDEEGICKT---AFELLFAFDEVISLGHKENVTVAQVKQYCEMESHEEKLHKLVVQSKINETKDV 158 (523)
Q Consensus 82 ~L~~l~~il~~y~g~l~E~~I~~n---iyel~~~lDEiid~G~pq~t~~~~lk~~i~m~s~ee~i~~~~~~~ke~eak~~ 158 (523)
||+++++++.+||+.+.|+.|++| +||| |||++||||||+|+.+.|++||.++++.-.
T Consensus 81 ~l~~~~~v~~~y~~~l~e~si~~n~vlvyEl---Lde~mDFGypQ~t~s~iL~~yi~~~~~~l~---------------- 141 (424)
T KOG0937|consen 81 FLYAVADVFGDYLSELEEESIRDNFVLVYEL---LDEVMDFGYPQTTDSEILKNYITQKANRLQ---------------- 141 (424)
T ss_pred HHHHHHHHHHHHhccCCccceecchHHHHHH---HHHHhccCCcccchHHHHHHHhccccccee----------------
Confidence 999999999999999999999999 8999 999999999999999999999999532100
Q ss_pred HHhhhhhhhhhhhhhccCCCCCccccccCCCCccccccccccccCCCCCCCCCCCcccccccccccccCCCCCCCCCCCC
Q 042402 159 MKRKASEIDKSKIEKNRGDKGGFMSLQSMGSGRIESSFSDMSISSGGGGFGSGSGFGLATTDVETFSSKSKGRPPSSANA 238 (523)
Q Consensus 159 ~k~~a~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~s~~~~~~~~p~~~~~~ 238 (523)
.. .. + ++ + ..+. .+
T Consensus 142 ---------~~-----~~-~---------------------------~p---------~-------------avtn--av 155 (424)
T KOG0937|consen 142 ---------DA-----QP-R---------------------------PP---------L-------------AVTN--AV 155 (424)
T ss_pred ---------ec-----CC-C---------------------------CC---------c-------------cccc--ce
Confidence 00 00 0 00 0 0000 12
Q ss_pred CCCCcCccccccCCchhhhhhhhhccceeecccCccccccccccCCCCCCCCeEEEEEEEEEEEEecCCCeEEEEEEEEE
Q 042402 239 PPKGLGMQLGKSQRTNQFLESLKAEGEVILEDVKPIAGQSRAAAAAPPLTDPITLTVEEKINVSLKRDGGMSNFDVQGTL 318 (523)
Q Consensus 239 ~~~~~gm~lgk~~~~n~~~~~l~~e~~~~~~~~~~~~~~~~~~~~~~~~~neI~vdV~Ekv~~~~~~~G~v~~~eV~G~i 318 (523)
.||..|+++| +||||+||+|+|+++++++|.++.++|.|+|
T Consensus 156 sWrs~gi~~~---------------------------------------KnevflDViE~Vs~l~~~~G~vl~s~i~G~I 196 (424)
T KOG0937|consen 156 SWRSEGIYYG---------------------------------------KNEVFLDVIESVSLLYDSNGIVLLSEIVGTI 196 (424)
T ss_pred eecccccccc---------------------------------------cceEEEEhhhhhhHhhhcCCcEEEeeeeeEE
Confidence 3787787543 3699999999999999999999999999999
Q ss_pred EEEEecCCCceEEEEeeCCCC-------------CCCCcccccccCcccccccceEEEeCCCCCccccccccccCCCCCc
Q 042402 319 SLQILNQEDGLIQVQIETGGN-------------PGILFKTHPNMNKELFTHENILGLKDPNRPFPQAKLWRMQSADESM 385 (523)
Q Consensus 319 ~~~~~lsg~p~~~l~ln~~~~-------------~~~d~~fHpcVd~~~f~~~r~Isf~pPdg~F~L~~~yr~~~~d~~~ 385 (523)
.||++|+|||+++|+||+... ..+|++||+||++++|++||+|+|+||||+|+|| +||+++ ...
T Consensus 197 ~~k~~LsGmPelrl~ln~~~~~~~~~~~~~s~~v~ledi~fh~~v~l~~fd~dr~i~FiPPdGeF~Lm-~Y~ls~--~vk 273 (424)
T KOG0937|consen 197 KLKCYLSGMPELRLGLNDKVLFDKQGPRSKSKGVELEDIKFHECVRLSRFDNDRTISFIPPDGEFELM-RYRLST--HVK 273 (424)
T ss_pred EEEEEcCCCceeeeecCcccccccccccccCcceEeeecccceeechhhccCCceEEecCCCCceEEE-EEEecC--CCC
Confidence 999999999999999997521 2389999999999999999999999999999999 899988 344
Q ss_pred CCeEEEEEEEeeCC---eEEEEEEEEecCCceeeeEEEEecCCCCCCCCeEEeecceEEEECCCCEEEEEEceecC-CCc
Q 042402 386 VPLTINCWPSVSGN---ETYVSIEYEASTMFDLRNVVISVPLPALREAPSVRQIDGEWRYDSRNSVLEWTILLIDN-SNR 461 (523)
Q Consensus 386 lP~~i~~~~~~~~~---~~~v~i~~~~~~~~~~~~V~V~iPlP~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~i~~-~~~ 461 (523)
+.+.+.......+. ++.++++..|+.+.++++|.|.||+|..++.+.+....|+++|+++++.|+|+|+++.| .+.
T Consensus 274 Pli~~~~~~~~~~~~ri~i~~K~~~~fk~~~~a~~v~I~iP~P~~a~~~~fk~s~G~~~~~~e~~~l~W~I~~~~gg~e~ 353 (424)
T KOG0937|consen 274 PLIWFYQLIEEHSRSRIEVMVKLREQFKSRSSANNVEICIPVPDDASSPSFKTSLGSAKYDPEKSALRWTIKKFVGGKEY 353 (424)
T ss_pred CeEEeeeeeeeccceeEEEEEechhhcCCccccceEEEEeeCCCccccceEeccCCceeeecccceEEEEeccccCCceE
Confidence 44444444433332 66777788888889999999999999989999999999999999999999999999998 789
Q ss_pred eEEEEEEeCC---CC--CCCCCCeEEEEEecc-cccCceEeEEEECC-CCCCCee-eEEEEEEeeceEE
Q 042402 462 SGSMEFVVPP---AD--SSSFFPISVRFSATS-TYSDLKVVNIIPLR-GGAPPKF-SQRTVLITENYQV 522 (523)
Q Consensus 462 s~s~ef~~~~---~~--~~~~~Pi~v~F~ip~-t~Sgl~V~~l~i~~-~~~~i~~-~~~~~~~~~~y~i 522 (523)
++++++.++. .. .....||+|+|+||+ |.||++|+|+++.+ ..+...+ +.+++..++.|++
T Consensus 354 ~~r~~~~lp~~~~e~~~~~~~~pi~v~FeIp~~T~SgiqVrylki~ep~~~y~s~~WVRy~T~s~~Y~~ 422 (424)
T KOG0937|consen 354 SLRARMDLPSEEHEEQCTEGLGPIKVKFEIPYFTVSGIQVRYLKIIEPKSQYQSLPWVRYNTQSGPYEI 422 (424)
T ss_pred EEEEeecCCccccCCCCcccCCceEEEEEecccccCCeEEEEEEecccccCCCccceEEEEccCCceEe
Confidence 9999999873 22 467899999999999 99999999999999 4455544 5899999999987
No 4
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.2e-58 Score=455.39 Aligned_cols=402 Identities=15% Similarity=0.180 Sum_probs=332.1
Q ss_pred eEEEEEEEcCCCCEEEEEcce--ecchHHHHHHHhhhchhhcCCCCCcEEEeCCEEEEEEEcCCEEEEEEEcCCCCHHHH
Q 042402 2 VVLAASIVSKSGKILVSRQFV--DMSRIRIEGLLAAFPKLVGTGKQHTYVETENVRYVYQPIEALYLLLVTNKQSNILED 79 (523)
Q Consensus 2 ~v~s~~Il~~~G~~lisR~yr--~~~r~~~e~~l~~F~~~i~~~~~~p~i~~~~~~yvy~~~~~ly~v~~t~~n~n~~~~ 79 (523)
+++|+|+.|.+|+++++++++ ..+|+.+..++..|.+.......+|++..+.+.|+-+-++++||+++++..+.|+.+
T Consensus 1 mi~siflidtsg~l~lek~~~g~t~~rsic~~f~e~~~~~~~~e~~ppvi~~p~hylfsv~~~~i~~~~~st~e~pPL~~ 80 (418)
T KOG2740|consen 1 MILSIFLIDTSGDLLLEKHLKGSTVVRSICDYFFEDQSSDDDLEHVPPVISTPHHYLFSVYRDLIFFCAVSTVETPPLMV 80 (418)
T ss_pred CeeEEEEEcCCchhhhhHhhCCceeeeehHHHHHHhhhhccccccCCceecCCceeeeeeeccCcEEEEEEeccCCChhH
Confidence 479999999999999999999 666888888766665555545567778887777777888999999999999999999
Q ss_pred HHHHHHHHHHHHhhcCCCChhhHHhh---HHHHHHhHHhHHhCCeecccCHHHHHHHhhccchHHHHHHHHhhhcchhhh
Q 042402 80 LETLRLLSKLVPEYSYSLDEEGICKT---AFELLFAFDEVISLGHKENVTVAQVKQYCEMESHEEKLHKLVVQSKINETK 156 (523)
Q Consensus 80 le~L~~l~~il~~y~g~l~E~~I~~n---iyel~~~lDEiid~G~pq~t~~~~lk~~i~m~s~ee~i~~~~~~~ke~eak 156 (523)
+|||||+++++++|||+++|..|++| |||| ||||+|+|||..|++++||+.|..+|.-.+...
T Consensus 81 iefL~rv~dv~~eyFg~~s~~~Ik~N~~vv~el---l~emiDnGfpl~tE~NiLke~i~pps~l~~~~~----------- 146 (418)
T KOG2740|consen 81 IEFLHRVVDVLLEYFGGLSESKIKDNVVVVYEL---LDEMIDNGFPLVTEPNILKELIPPPSFLSKKFN----------- 146 (418)
T ss_pred HHHHHHHHHHHHHHhcccCHhHhhcceeeHHHH---HHHHHHcCCCcccChhHHHhhcCChHHHHHHHh-----------
Confidence 99999999999999999999999999 8999 999999999999999999999887655432110
Q ss_pred HHHHhhhhhhhhhhhhhccCCCCCccccccCCCCccccccccccccCCCCCCCCCCCcccccccccccccCCCCCCC-CC
Q 042402 157 DVMKRKASEIDKSKIEKNRGDKGGFMSLQSMGSGRIESSFSDMSISSGGGGFGSGSGFGLATTDVETFSSKSKGRPP-SS 235 (523)
Q Consensus 157 ~~~k~~a~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~s~~~~~~~~p~-~~ 235 (523)
+..| +.+++. ..|+ +.
T Consensus 147 -----------------svTg-----------~~n~~~-----------------------------------~lPtg~~ 163 (418)
T KOG2740|consen 147 -----------------SVTG-----------NSNVSD-----------------------------------TLPTGAL 163 (418)
T ss_pred -----------------hhhc-----------cccccc-----------------------------------cCCCccc
Confidence 0000 001111 0111 23
Q ss_pred CCCCCCCcCccccccCCchhhhhhhhhccceeecccCccccccccccCCCCCCCCeEEEEEEEEEEEEecCCCeEEEEEE
Q 042402 236 ANAPPKGLGMQLGKSQRTNQFLESLKAEGEVILEDVKPIAGQSRAAAAAPPLTDPITLTVEEKINVSLKRDGGMSNFDVQ 315 (523)
Q Consensus 236 ~~~~~~~~gm~lgk~~~~n~~~~~l~~e~~~~~~~~~~~~~~~~~~~~~~~~~neI~vdV~Ekv~~~~~~~G~v~~~eV~ 315 (523)
...|||..|. +|.+||+||||.|+++++++++|.++..+|+
T Consensus 164 s~VPWR~~~~---------------------------------------Ky~nNE~yvdvlEeidai~~k~gslv~~eI~ 204 (418)
T KOG2740|consen 164 SNVPWRTAGV---------------------------------------KYTNNEAYVDVLEEIDAIVDKKGSLVFGEIQ 204 (418)
T ss_pred ccccccccCc---------------------------------------ccccchhhhhhhheeheEecCCCCEEEEEEE
Confidence 3679997553 6888999999999999999999999999999
Q ss_pred EEEEEEEecCCCceEEEEeeCCCCCCCCcccccccCcccccccceEEEeCCCCCccccccccccCCCCCcCCeEEEEEEE
Q 042402 316 GTLSLQILNQEDGLIQVQIETGGNPGILFKTHPNMNKELFTHENILGLKDPNRPFPQAKLWRMQSADESMVPLTINCWPS 395 (523)
Q Consensus 316 G~i~~~~~lsg~p~~~l~ln~~~~~~~d~~fHpcVd~~~f~~~r~Isf~pPdg~F~L~~~yr~~~~d~~~lP~~i~~~~~ 395 (523)
|.+.|+|+|+|||++.|.|+++. ..+|++|||||++++|+++++|+|+||||.|+|+ +||+.......+|..+...++
T Consensus 205 g~vd~~~qLsgmPdltlsl~np~-~L~dvsfHpcVr~krwe~~~~lsFIPPDGkFrLl-sy~v~~~~~v~~pvyv~~~i~ 282 (418)
T KOG2740|consen 205 GIVDVCSQLSGMPDLTLSLNNPR-LLGDVSFHPCVRYKRWESHSVLSFIPPDGKFRLL-SYRVDAQNQVAIPVYVKNSIS 282 (418)
T ss_pred EEEEEEEeecCCCceEEEccCcc-ccCCcccccceeecccccccceEEcCCCCcEEEE-EEEEehhhccccceEEeeeec
Confidence 99999999999999999998854 5699999999999999999999999999999999 899987667789999999998
Q ss_pred eeCCe-EEEEEEEEec--CCceeeeEEEEecCCCCCCCCeEEeecceEEEECCCCEEEEEEceecC-CC--ceEEEEEEe
Q 042402 396 VSGNE-TYVSIEYEAS--TMFDLRNVVISVPLPALREAPSVRQIDGEWRYDSRNSVLEWTILLIDN-SN--RSGSMEFVV 469 (523)
Q Consensus 396 ~~~~~-~~v~i~~~~~--~~~~~~~V~V~iPlP~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~i~~-~~--~s~s~ef~~ 469 (523)
..++. +.+.+..... ....++-+.|++..|............|++.+++..+.+-|+++++.. .- ..|.++.+-
T Consensus 283 l~~~~~~ri~~tvg~~~~~gK~ie~itVt~~~pn~i~~~~k~~~~g~~~~~~~~k~l~W~~~~i~tg~lp~Lkg~~~~e~ 362 (418)
T KOG2740|consen 283 LDSNHQGRISLTVGPKKKMGKTIELITVTVQDPNEIAYASKILTHGTFTNSIIMKQLTWTFGSIATGKLPVLKGTINLEP 362 (418)
T ss_pred cCCCceEEEEEeccccccccceeEeEEEEecCccceeeeecccccceeEeecccceeEEEeecccCCcccccccccccCC
Confidence 88764 3444333333 235788889999999987777777899999999999999999999875 22 345555443
Q ss_pred CCCCCCCCCCeEEEEEecc-cccCceEeEEEECCCCCCCeee-EEEEEEeeceEE
Q 042402 470 PPADSSSFFPISVRFSATS-TYSDLKVVNIIPLRGGAPPKFS-QRTVLITENYQV 522 (523)
Q Consensus 470 ~~~~~~~~~Pi~v~F~ip~-t~Sgl~V~~l~i~~~~~~i~~~-~~~~~~~~~y~i 522 (523)
......++.-++++|.+.+ ++|||+|+.|++.+ +...+|. .++..++++|++
T Consensus 363 ~~sk~~~l~t~~Lqykiqg~alsglkVe~Ldm~~-~~~k~yKGvKy~t~agnfqv 416 (418)
T KOG2740|consen 363 GFSKKVDLPTLSLQYKIQGQALSGLKVERLDMYG-EPYKPYKGVKYKTKAGNFQV 416 (418)
T ss_pred CCCccccCcccceeeeeeeeeccceEEEeeeecC-CCCccccceEEEEeeeeEEE
Confidence 3456678899999999999 99999999999998 4556685 888999999987
No 5
>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=6.4e-46 Score=371.65 Aligned_cols=235 Identities=29% Similarity=0.447 Sum_probs=186.4
Q ss_pred CCCCCCeEEEEEEEEEEEEecCCCeEEEEEEEEEEEEEecCCCceEEEEeeCC---C---CCCCCcccccccCccccccc
Q 042402 285 PPLTDPITLTVEEKINVSLKRDGGMSNFDVQGTLSLQILNQEDGLIQVQIETG---G---NPGILFKTHPNMNKELFTHE 358 (523)
Q Consensus 285 ~~~~neI~vdV~Ekv~~~~~~~G~v~~~eV~G~i~~~~~lsg~p~~~l~ln~~---~---~~~~d~~fHpcVd~~~f~~~ 358 (523)
.+.+|||||||+|+++++++++|.+.+++|+|+|.|+++|+|+|+|+|.|+++ . ...+|++||||||+++|+++
T Consensus 9 ~~~~nei~vdv~E~i~~~~~~~G~~~~~~v~G~v~~~~~l~g~p~i~l~l~~~~~~~~~~~~l~~~~fH~cV~~~~~~~~ 88 (262)
T PF00928_consen 9 KYKKNEIFVDVVEKISAVLDRDGNILSSEVKGSVQCKSFLSGMPEIKLTLNNPLVVSKNGIKLDDVSFHPCVDLSKFESD 88 (262)
T ss_dssp --SSEEEEEEEEEEEEEEEETTSEEEEEEEEEEEEEEEE-SST-EEEEEESSSCCCTSSSBEESEEEEETTEECCCCCSH
T ss_pred ccccceEEEEEEEEEEEEEccCCcEEEEEEEEEEEEEEeCCCCCeEEEEecCccccccCceeeeceeeccccCccccccc
Confidence 45667999999999999999999999999999999999999999999999876 1 23489999999999999999
Q ss_pred ceEEEeCCCCCccccccccccCCCCCcCCeEEEEEEEeeC-CeEEEEEEE--EecCCceeeeEEEEecCCCCCCCCeEEe
Q 042402 359 NILGLKDPNRPFPQAKLWRMQSADESMVPLTINCWPSVSG-NETYVSIEY--EASTMFDLRNVVISVPLPALREAPSVRQ 435 (523)
Q Consensus 359 r~Isf~pPdg~F~L~~~yr~~~~d~~~lP~~i~~~~~~~~-~~~~v~i~~--~~~~~~~~~~V~V~iPlP~~~~~~~~~~ 435 (523)
|+|+|+||||.|+|| +||++. ...+||.++||+...+ +.+.+.+++ .++....++||.|+||+|..+..+++..
T Consensus 89 ~~i~f~PPdg~f~Ll-~Yr~~~--~~~~P~~i~~~~~~~~~~~~~v~i~~~~~~~~~~~~~~v~I~iplP~~~~~~~~~~ 165 (262)
T PF00928_consen 89 RVISFIPPDGEFTLL-RYRVSS--NSPLPFKITCWVSEKSSGRFEVTIELESNFPNKISLENVVIRIPLPPGTSSPSIES 165 (262)
T ss_dssp TEEEE---SEEEEEE-EEEEES--SS--SEEEEEEEEEETTTEEEEEEEEEE-S-TTSEEEEEEEEEE--TTEEEEEEEE
T ss_pred cceecCCCCceEEEE-EEEccC--CCCCCcEEEEEeccCCCceEEEEEEecccCCCCceeceEEEEeecCCccccceeee
Confidence 999999999999999 899987 5889999999998844 555555554 4555578999999999999777889999
Q ss_pred ecceEEEECCCCEEEEEEceecC-CCc--eEEEEEEeCCCCC--CCCCCeEEEEEecc-cccCceEeEEEECC--CCCCC
Q 042402 436 IDGEWRYDSRNSVLEWTILLIDN-SNR--SGSMEFVVPPADS--SSFFPISVRFSATS-TYSDLKVVNIIPLR--GGAPP 507 (523)
Q Consensus 436 ~~G~~~~~~~~~~l~W~I~~i~~-~~~--s~s~ef~~~~~~~--~~~~Pi~v~F~ip~-t~Sgl~V~~l~i~~--~~~~i 507 (523)
..|+++|+..++.|+|+|+++.+ .+. +|+++|....... ..++||+|+|++|+ ++|||+|++|++.+ ++..+
T Consensus 166 ~~G~~~~~~~~~~l~W~I~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~pi~v~F~~~~~~~Sgl~V~~l~v~~~~~~~~~ 245 (262)
T PF00928_consen 166 SDGSAEYDEEENALVWKIKKLPGGSESTLSGTLEFSSPSSVPSDWSFFPISVEFTIPGYTLSGLKVRSLDVVNEDENYKP 245 (262)
T ss_dssp SSSEEEEETGCTEEEEEEEEEETSEEEEEEEEEEEEEECCSS-S-----EEEEEEESTSETTT-EEEEEEEE-SSCGGGS
T ss_pred cCceEEEEccCCEEEEEECCccCcccccEEEEEEecCCCcccccccceeEEEEEEeCCcccCCCEEEEEEeEecCCCCCC
Confidence 99999999999999999999998 444 4555665543322 37999999999999 99999999999998 44555
Q ss_pred eeeEEEEEEeeceEE
Q 042402 508 KFSQRTVLITENYQV 522 (523)
Q Consensus 508 ~~~~~~~~~~~~y~i 522 (523)
..+.++++++++|+|
T Consensus 246 ~k~vky~t~s~~Y~i 260 (262)
T PF00928_consen 246 YKWVKYVTKSGSYEI 260 (262)
T ss_dssp EEEEEEEEEEEEEEE
T ss_pred cccEEEEEEcCcEEE
Confidence 557999999999998
No 6
>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=99.92 E-value=1.5e-24 Score=197.51 Aligned_cols=136 Identities=25% Similarity=0.335 Sum_probs=118.3
Q ss_pred eEEEEEEEcCCCCEEEEEcceecchHHHHHHHhhhchhhcC--CCCCcEEEeCCEEEEEEEcCCEEEEEEEcCCCCHHHH
Q 042402 2 VVLAASIVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGT--GKQHTYVETENVRYVYQPIEALYLLLVTNKQSNILED 79 (523)
Q Consensus 2 ~v~s~~Il~~~G~~lisR~yr~~~r~~~e~~l~~F~~~i~~--~~~~p~i~~~~~~yvy~~~~~ly~v~~t~~n~n~~~~ 79 (523)
+|.|++|+|++|+++++|+|++.+......+...+.+.+.. ...+|++.+++++++|+++++|||+++++.+.|++..
T Consensus 1 MI~~i~i~n~~G~~i~~k~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~dl~~~~v~~~~eNel~~ 80 (141)
T PF01217_consen 1 MIKAILILNSQGKRILSKYYRDVSEEERQKLFEKFIKKKSSRNSKQSPIFEHDNYRIVYKRYSDLYFVVVGDENENELLL 80 (141)
T ss_dssp SEEEEEEEETTSEEEEEEESSTSTSHHHHHHHHHHHHHHHTSSSSSTSEEEETTEEEEEEEETTEEEEEEESSTSBHHHH
T ss_pred CEEEEEEEcCCCCEEEehhcCCccHHHHHHHHHHHHHHHHhcccccceeeecccceeeeEeeccEEEEEEeecccchHHH
Confidence 36899999999999999999977766666666667666665 3468999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhcCCCChhhHHhhHHHHHHhHHhHHhCCeecccCHHHHHHHhhcc
Q 042402 80 LETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLGHKENVTVAQVKQYCEME 137 (523)
Q Consensus 80 le~L~~l~~il~~y~g~l~E~~I~~niyel~~~lDEiid~G~pq~t~~~~lk~~i~m~ 137 (523)
+++||+++++++.|||.++|.+|++|...++.+||||+|+|+|++|+++.|...+.|.
T Consensus 81 ~e~l~~~v~~l~~~~~~v~e~~i~~N~~~v~~~LDEiid~G~i~etd~~~I~~~v~~~ 138 (141)
T PF01217_consen 81 LEFLHRLVEVLDDYFGNVSEKDILENFDLVYLILDEIIDGGIILETDPNVILKRVTMQ 138 (141)
T ss_dssp HHHHHHHHHHHHHHHSS-SHHHHHHTHHHHHHHHHHHEETTEES--THHHHHHHHHHC
T ss_pred HHHHHHhhhhhhhhhccccHHHHHHCHHHHHHHHHHHHhCCEEEECCHHHHHHHHHHh
Confidence 9999999999999999999999999954444459999999999999999999888873
No 7
>KOG2677 consensus Stoned B synaptic vesicle biogenesis protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.82 E-value=5.5e-21 Score=200.68 Aligned_cols=235 Identities=17% Similarity=0.197 Sum_probs=186.6
Q ss_pred CCCCCCCeEEEEEEEEEEEEecCCCeEEEEEEEEEEEEEecCCCceEEEEeeCCCC--------------------CCCC
Q 042402 284 APPLTDPITLTVEEKINVSLKRDGGMSNFDVQGTLSLQILNQEDGLIQVQIETGGN--------------------PGIL 343 (523)
Q Consensus 284 ~~~~~neI~vdV~Ekv~~~~~~~G~v~~~eV~G~i~~~~~lsg~p~~~l~ln~~~~--------------------~~~d 343 (523)
..|..+||-|||.......++.+|.++...|.-.|.|-++|+|.++|+|+||+-.. +..+
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 47888999999999999999999999999999999999999999999999997411 2378
Q ss_pred cccccccCcccccccceEEEeCCCC-CccccccccccCCCCCcCCeEEEEEEEeeCCeEEEEEEEE----ecC------C
Q 042402 344 FKTHPNMNKELFTHENILGLKDPNR-PFPQAKLWRMQSADESMVPLTINCWPSVSGNETYVSIEYE----AST------M 412 (523)
Q Consensus 344 ~~fHpcVd~~~f~~~r~Isf~pPdg-~F~L~~~yr~~~~d~~~lP~~i~~~~~~~~~~~~v~i~~~----~~~------~ 412 (523)
|.||-|||.+.|+++|+|.|.|+|| .|+|| ++|.--. ...+||++.-.....|.++.|.+... +.. +
T Consensus 662 ~~FH~cVn~~eF~~srVI~F~PlDaCrFElM-RFrt~~~-~~~lpftlks~~~V~Ga~VEvq~~~~mat~~qr~rd~~~~ 739 (922)
T KOG2677|consen 662 CRFHGCVNEDEFHNSRVILFNPLDACRFELM-RFRTVFA-EKTLPFTLKSATSVNGAEVEVQSWLRMATGFQRNRDPLTQ 739 (922)
T ss_pred eeeecccchhhccccceEEecCcccceeeee-eeeeecC-CCcCceeeeeeeeeccceeehHHHHHHHhhhhhccCcccc
Confidence 9999999999999999999999998 89999 7887554 34799999988888775544443221 111 3
Q ss_pred ceeeeEEEEecCCCC--------------------------------CCCCeEEeecceEEEECCCCEEEEEEceecCCC
Q 042402 413 FDLRNVVISVPLPAL--------------------------------REAPSVRQIDGEWRYDSRNSVLEWTILLIDNSN 460 (523)
Q Consensus 413 ~~~~~V~V~iPlP~~--------------------------------~~~~~~~~~~G~~~~~~~~~~l~W~I~~i~~~~ 460 (523)
..++||.|++|+|+. .+.+.+.+.-|+++|...=+.|+|+|+++..+|
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 579999999999982 123566677899999999999999999998754
Q ss_pred ce------EEEEEEeCC--CCCCCCCC-eEEEEEecc-cccCceEeEEEECCCC---CCCeeeEEEEEEeece
Q 042402 461 RS------GSMEFVVPP--ADSSSFFP-ISVRFSATS-TYSDLKVVNIIPLRGG---APPKFSQRTVLITENY 520 (523)
Q Consensus 461 ~s------~s~ef~~~~--~~~~~~~P-i~v~F~ip~-t~Sgl~V~~l~i~~~~---~~i~~~~~~~~~~~~y 520 (523)
+. +.+.|.+.+ ..+.+|.| +.|+|..|. ++|.-.|+.|-++... +-++|+..+..+++=|
T Consensus 820 sa~~hpHcl~c~lELgSd~evPs~f~p~~~V~FsmP~t~aS~t~VRSisVE~~~~v~K~V~y~A~Y~yqv~l~ 892 (922)
T KOG2677|consen 820 SASGHPHCLFCHLELGSDREVPSRFAPHVNVEFSMPTTSASKTSVRSISVEDKTDVRKWVNYSAHYSYQVALG 892 (922)
T ss_pred cccCCCeeEEEEEeccccccCchhhccccceeeeccccccccceeeeeeccccccHHHHHhhhhheeeeeeec
Confidence 22 445555532 33455655 589999999 9999999999998853 3456666666665544
No 8
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=99.81 E-value=2e-19 Score=156.74 Aligned_cols=129 Identities=19% Similarity=0.253 Sum_probs=116.3
Q ss_pred EEEEEEEcCCCCEEEEEcceecchHHHHHHHhhhchhhcC--CCCCcEEEeCCEEEEEEEcCCEEEEEEEcCCCCHHHHH
Q 042402 3 VLAASIVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGT--GKQHTYVETENVRYVYQPIEALYLLLVTNKQSNILEDL 80 (523)
Q Consensus 3 v~s~~Il~~~G~~lisR~yr~~~r~~~e~~l~~F~~~i~~--~~~~p~i~~~~~~yvy~~~~~ly~v~~t~~n~n~~~~l 80 (523)
|..+.|.|++|++++.|||.+++...-..+++.-+.+|.+ .+++++++..+.+.||+++.+|||+++.+..+|.+.+|
T Consensus 2 i~~vli~nrqgk~RL~K~yt~~~~~e~~kli~~i~~lIs~R~~ke~N~~e~k~~kiVYrrYA~LyF~f~Vd~~dnEl~iL 81 (152)
T COG5030 2 IKFVLIFNRQGKPRLVKWYTPVSDPEQAKLIADIYELISARKPKESNFIEGKNEKIVYRRYATLYFVFGVDNDDNELIIL 81 (152)
T ss_pred eEEEEEEcCCCceeeeEeeccCCcHHHHHHHHHHHHHHHcCCchhcccccccCcEEEeeecCcEEEEEEEcCCCCcchHH
Confidence 5789999999999999999977743333466667788887 46889999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhcCCCChhhHHhhHHHHHHhHHhHHhCCeecccCHHHHH
Q 042402 81 ETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLGHKENVTVAQVK 131 (523)
Q Consensus 81 e~L~~l~~il~~y~g~l~E~~I~~niyel~~~lDEiid~G~pq~t~~~~lk 131 (523)
+.+|.|+++++.|||.+||.+++.|.++++.+||||+.+|-.++++++.+-
T Consensus 82 ~lIh~FVE~lDr~FgnVCELdlIFNF~kv~~ILdE~i~gG~i~Es~~~~vl 132 (152)
T COG5030 82 ELIHNFVEILDRFFGNVCELDLIFNFQKVYAILDEMILGGEIIESSKNEVL 132 (152)
T ss_pred HHHHHHHHHHHHHhccceeeEeEeeHHHHHHHHHHHHhCCeeeecCHHHHH
Confidence 999999999999999999999999988888889999999999999987755
No 9
>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.72 E-value=4.1e-17 Score=138.51 Aligned_cols=133 Identities=18% Similarity=0.281 Sum_probs=106.5
Q ss_pred EEEEEEEcCCCCEEEEEcceecchHHHHHHHhhhchhhcC--CCCCcEEEeCCEEEE-EEEcCCEEEEEEEcCCCCHHHH
Q 042402 3 VLAASIVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGT--GKQHTYVETENVRYV-YQPIEALYLLLVTNKQSNILED 79 (523)
Q Consensus 3 v~s~~Il~~~G~~lisR~yr~~~r~~~e~~l~~F~~~i~~--~~~~p~i~~~~~~yv-y~~~~~ly~v~~t~~n~n~~~~ 79 (523)
|.=+.|.|++|+++++|||...+...-..+++.-.+++.. .+..++++..+.+-+ +++++||||+.+++..+|.+..
T Consensus 2 i~FILiqNr~Gk~RLak~yv~~dd~ek~~~~~~vh~lvs~Rd~K~~~~~~~~~~~~~~~rryagLyf~~~vd~tDnelay 81 (143)
T KOG0935|consen 2 IRFILIQNRAGKTRLAKWYVQFDDDEKQKLIEEVHALVTVRDAKHTNFVEFRNFKIIYRRRYAGLYFCICVDVTDNELAY 81 (143)
T ss_pred eEEEEEEccccceeheeeeeccCchHHHHHHHHHHHHHhhccchhhhheeeeeceEEEEEeeCCEEEEEEEecCCchHHH
Confidence 4567899999999999999966633334455566777776 333344444444444 4699999999999999999999
Q ss_pred HHHHHHHHHHHHhhcCCCChhhHHhhHHHHHHhHHhHHhCCeecccCHHHHHHHhh
Q 042402 80 LETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLGHKENVTVAQVKQYCE 135 (523)
Q Consensus 80 le~L~~l~~il~~y~g~l~E~~I~~niyel~~~lDEiid~G~pq~t~~~~lk~~i~ 135 (523)
||.+|+|+++++.|||++||.++..|.|.++-++|||+-.|..|+|+...+.+-+.
T Consensus 82 Le~IHlFVEvLd~fF~NVCELDlvFNFyKVy~i~DEm~l~GEi~Etsk~~vlerl~ 137 (143)
T KOG0935|consen 82 LEHIHLFVEVLDEFFHNVCELDLVFNFYKVYTIVDEMFLAGEIRETSKTKVLERLL 137 (143)
T ss_pred HHHHHHHHHHHHHHhccccceeeeeeeeeHHHHHHHHHHhhhhhhhhHHHHHHHHH
Confidence 99999999999999999999999999666666699999999999999877654443
No 10
>KOG0934 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.70 E-value=2.2e-17 Score=143.84 Aligned_cols=124 Identities=23% Similarity=0.269 Sum_probs=105.1
Q ss_pred EEEEEEEcCCCCEEEEEcceecc---hHHHHHHHhhhchhhcC--CCCCcEEEeCCEEEEEEEcCCEEEEEEEcCCCCHH
Q 042402 3 VLAASIVSKSGKILVSRQFVDMS---RIRIEGLLAAFPKLVGT--GKQHTYVETENVRYVYQPIEALYLLLVTNKQSNIL 77 (523)
Q Consensus 3 v~s~~Il~~~G~~lisR~yr~~~---r~~~e~~l~~F~~~i~~--~~~~p~i~~~~~~yvy~~~~~ly~v~~t~~n~n~~ 77 (523)
|...-+.+++|++++++||..++ |..+++- -.+.+.+ .++|.++++.+.+.||++++.|||++....+.|.+
T Consensus 2 i~f~LlvsrQGk~rL~k~y~~~~~~er~~i~re---~i~~~Lar~pk~csfie~kd~kvVyrryasl~f~~~v~~~dNEL 78 (145)
T KOG0934|consen 2 IKFFLLVSRQGKTRLQKWYEALSIKERKKIERE---LIKSVLARKPKMCSFIEYKDEKVVYRRYASLFFCVGVEDNDNEL 78 (145)
T ss_pred eEEEEEEeccCceehhHHHhhhcHHHHHHHHHH---HHHHHHhCCcccccchhccCceehhhhhhhEEEEEEEecCCchh
Confidence 45677889999999999999777 3334442 2333443 46889999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhcCCCChhhHHhhHHHHHHhHHhHHhCCeecccCHHH
Q 042402 78 EDLETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLGHKENVTVAQ 129 (523)
Q Consensus 78 ~~le~L~~l~~il~~y~g~l~E~~I~~niyel~~~lDEiid~G~pq~t~~~~ 129 (523)
.+||++|+++++++.|||++||.+|+.|.-+.+|+|||++-.|-.|+++.+.
T Consensus 79 ~~LE~IH~~vE~lDkYFg~VCELDiiFNfekay~ILde~~~~g~~~e~~k~~ 130 (145)
T KOG0934|consen 79 AILEFIHNYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEIQETSKND 130 (145)
T ss_pred hHHHHHHHHHHHHHHHhccceeeEEEEehHhHHHHHHHHhcCcchHhhhccc
Confidence 9999999999999999999999999999766667799999999888776543
No 11
>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.52 E-value=1.2e-13 Score=122.17 Aligned_cols=134 Identities=13% Similarity=0.224 Sum_probs=112.5
Q ss_pred eEEEEEEEcCCCCEEEEEcceecchHHHHHHHhhhchhhcC--CCCCcEEEe------CCEEEEEEEcCCEEEEEEEcCC
Q 042402 2 VVLAASIVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGT--GKQHTYVET------ENVRYVYQPIEALYLLLVTNKQ 73 (523)
Q Consensus 2 ~v~s~~Il~~~G~~lisR~yr~~~r~~~e~~l~~F~~~i~~--~~~~p~i~~------~~~~yvy~~~~~ly~v~~t~~n 73 (523)
+|.|+.|+|.+|++++.|.|..++...-..++..-+.++.. ...++|++. ...+.+|+.+.-||||.+.+..
T Consensus 1 MI~AvlifNn~gkPRL~KFY~p~~~~~Qq~lir~vf~lvs~R~~n~~nFLe~~~l~g~~d~rlIYrhYATLYFvfvvD~s 80 (182)
T KOG0936|consen 1 MIKAVLIFNNKGKPRLVKFYTPVDEEKQQQLIREVFHLVSKRPDNVCNFLEGNSLIGGSDNRLIYRHYATLYFVFVVDSS 80 (182)
T ss_pred CeeEEEEecCCCCcceeeecCcCChHHHHHHHHHHHHHHHcCCchHhhhhccccccCCccceeehheeeeEEEEEEEcCC
Confidence 36899999999999999999977744444444444555654 235677664 3689999999999999999999
Q ss_pred CCHHHHHHHHHHHHHHHHhhcCCCChhhHHhhHHHHHHhHHhHHhCCeecccCHHHHHHHhh
Q 042402 74 SNILEDLETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLGHKENVTVAQVKQYCE 135 (523)
Q Consensus 74 ~n~~~~le~L~~l~~il~~y~g~l~E~~I~~niyel~~~lDEiid~G~pq~t~~~~lk~~i~ 135 (523)
.+.+.+|++++.|++.|+..|..+||.+++.|.-+++.+|+||+.+|...+|+.+.|-.-++
T Consensus 81 EsEL~iLDLIQvfVEtLDkCF~nVcELDliF~~~k~h~iL~EiV~GGmVlETn~neIv~av~ 142 (182)
T KOG0936|consen 81 ESELGILDLIQVFVETLDKCFENVCELDLIFNWQKVHAILAEIVMGGMVLETNMNEIVAAVD 142 (182)
T ss_pred cchhHHHHHHHHHHHHHHHHHHhhhhhhheeeHHHHHHHHHHHHhCCeEEeccHHHHHHHHH
Confidence 99999999999999999999999999999999777777799999999999999988765444
No 12
>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=99.15 E-value=5.8e-09 Score=104.25 Aligned_cols=226 Identities=17% Similarity=0.210 Sum_probs=128.2
Q ss_pred CeEEEEEEEEEEEEecCCCeEEEEEEEEEEEEEecCCC------ceEEEEeeCCCCCCCCcccccccCcccccccceEEE
Q 042402 290 PITLTVEEKINVSLKRDGGMSNFDVQGTLSLQILNQED------GLIQVQIETGGNPGILFKTHPNMNKELFTHENILGL 363 (523)
Q Consensus 290 eI~vdV~Ekv~~~~~~~G~v~~~eV~G~i~~~~~lsg~------p~~~l~ln~~~~~~~d~~fHpcVd~~~f~~~r~Isf 363 (523)
++-.-|.|.||+.+ ++|.+.++.|.|+|.|.-.-.-. +.+.+.|++.. ..+++...+..=...-.++....|
T Consensus 2 gl~asi~E~VnA~F-k~g~~~~v~v~GEv~ls~~~~~~~~~~~~~~l~~rl~n~~-~le~i~pN~~~v~~~~~~~~~f~~ 79 (257)
T PF10291_consen 2 GLNASITETVNAYF-KGGQLSKVKVTGEVALSYPAGISSSLTSPPPLSFRLNNFS-RLEKIAPNPQFVSSSSQSDGEFWL 79 (257)
T ss_dssp EEEEEEEEEEEEEE-ETTEEEEEEEEEEEEEEEE--SSS-----SEEEEEEETGG-GEEEEEE-TTTE--EEEETTEEEE
T ss_pred ceeEEEEEEEEEEE-ECCcEEEEEEEEEEEEecCCChhhcccCCCcEEEEEcCcc-hhceeecCHhHeecCCCCCCcEEE
Confidence 35678999999999 88999999999999998654433 45688887532 223332222211101112223333
Q ss_pred eCCC--CCc--cccccccccCCCC--CcCCeEEEEEEEeeCCeEEEEEEEEecCC-----ceeeeEEEEecCCCCCCCCe
Q 042402 364 KDPN--RPF--PQAKLWRMQSADE--SMVPLTINCWPSVSGNETYVSIEYEASTM-----FDLRNVVISVPLPALREAPS 432 (523)
Q Consensus 364 ~pPd--g~F--~L~~~yr~~~~d~--~~lP~~i~~~~~~~~~~~~v~i~~~~~~~-----~~~~~V~V~iPlP~~~~~~~ 432 (523)
.++- ... ..+ .|++..... ..+||.+.+..........|.|.|.+++. ..++||+|.+|+... ....
T Consensus 80 n~~~l~~~~~~~al-KYqv~~~~~~~~~~Pl~l~~~Wk~e~~~tsl~l~Y~~Np~~~~~~~~L~nv~~~v~l~g~-~~ts 157 (257)
T PF10291_consen 80 NMSALTSHLPKQAL-KYQVHSDPSNLSSVPLILKPVWKCEPSQTSLILDYKLNPDAFASPVPLENVVFSVPLDGG-RATS 157 (257)
T ss_dssp -TTTTBT-E-EEEE-EEEEES--------SEEEEEEEEE-SSEEEEEEEEEE-TTT--E-EEEEEEEEEEEB-SS--EEE
T ss_pred ehHHhhhhhhhceE-EEEEeccccccCCCCeEEEeEEEeCCceEEEEEEEEeChhhccccceeeeEEEEEEcCCc-cccc
Confidence 3321 111 112 388876432 67899998877777778888888888772 579999999999874 1112
Q ss_pred EEeecceEEEECCCCEEEEEEceecC-CC---ceEEEEEEeCCCCCCCCCCeEEEEEec-c-cccCceEeEEEECCC---
Q 042402 433 VRQIDGEWRYDSRNSVLEWTILLIDN-SN---RSGSMEFVVPPADSSSFFPISVRFSAT-S-TYSDLKVVNIIPLRG--- 503 (523)
Q Consensus 433 ~~~~~G~~~~~~~~~~l~W~I~~i~~-~~---~s~s~ef~~~~~~~~~~~Pi~v~F~ip-~-t~Sgl~V~~l~i~~~--- 503 (523)
+.+ .-...|..+++.+.|+|+.+.- ++ ..+.++|....... .-.+|.++|++. . +.||+.|.-+.-.++
T Consensus 158 ~~s-kP~g~~~~e~~ri~Wrl~el~~~~~~~~~kL~ARf~~~~~~~-~p~~v~vkF~~~~~~~~sg~~i~~~~~~~~~dp 235 (257)
T PF10291_consen 158 AQS-KPQGTWNKEKNRITWRLPELSLTSEGEGGKLIARFMTSGGPS-RPGGVEVKFEIEGGSTLSGLGISLVYQDDEEDP 235 (257)
T ss_dssp EEE-SSS--B-SSS-EEEEE-SSEEEETT---EEEEEEEEESS-----SS-EEEEEEE---S-SS----EEEEEESSS-T
T ss_pred ccc-CCCccccCCCcEEEEECCcccccCCCCCceEEEEEECCCCCC-CCceEEEEEEEcCCCcccCcEEEEeecccccCC
Confidence 222 2224777899999999999874 22 46677788754333 778999999999 6 899999988833222
Q ss_pred -CCCC-eeeEEEEEEeeceE
Q 042402 504 -GAPP-KFSQRTVLITENYQ 521 (523)
Q Consensus 504 -~~~i-~~~~~~~~~~~~y~ 521 (523)
|... .--+.+.|.+|+|.
T Consensus 236 ~~~~w~~~~~~r~~~sGkY~ 255 (257)
T PF10291_consen 236 PGGGWRLVLVKRKLVSGKYI 255 (257)
T ss_dssp T----EE-EEEEEEEEEEEE
T ss_pred CCCcceEEEEEEEEeeeEEe
Confidence 2222 33589999999996
No 13
>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.74 E-value=1.3e-07 Score=85.08 Aligned_cols=140 Identities=19% Similarity=0.228 Sum_probs=113.9
Q ss_pred eEEEEEEEcCCCCEEEEEcce-ecchHHHHHHHhhhchhhcC--CC-CCcEEEeCCEEEEEEEcCCEEEEEEEcCCCCHH
Q 042402 2 VVLAASIVSKSGKILVSRQFV-DMSRIRIEGLLAAFPKLVGT--GK-QHTYVETENVRYVYQPIEALYLLLVTNKQSNIL 77 (523)
Q Consensus 2 ~v~s~~Il~~~G~~lisR~yr-~~~r~~~e~~l~~F~~~i~~--~~-~~p~i~~~~~~yvy~~~~~ly~v~~t~~n~n~~ 77 (523)
.|-++.|+|.+|+.+..|.|- +.+...-|. .+|-+.+=+ ++ ..-+.-.+|...+|...-+|||-++-..+.|.+
T Consensus 8 ~vk~iliLD~~G~Ri~aKYY~~~~~s~vkeq--kaFEK~lF~KT~kt~~eI~~ldg~~vvYk~~~Dl~fyv~G~~~ENEl 85 (175)
T KOG3343|consen 8 TVKAILILDSDGKRILAKYYDDPHPSTVKEQ--KAFEKNLFSKTSKTESEILLLDGNTVVYKSVIDLHFYVVGSEEENEL 85 (175)
T ss_pred hhheEEEEcCCCCEeeeeecCCCcchhHHHH--HHHHHHHhcccccccceeEEecCcEEEEEecccEEEEEecCcchhHH
Confidence 356899999999999999999 544323332 236666544 22 345888899999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhcC-CCChhhHHhhHHHHHHhHHhHHhCCeecccCHHHHHHHhhccchHHHH
Q 042402 78 EDLETLRLLSKLVPEYSY-SLDEEGICKTAFELLFAFDEVISLGHKENVTVAQVKQYCEMESHEEKL 143 (523)
Q Consensus 78 ~~le~L~~l~~il~~y~g-~l~E~~I~~niyel~~~lDEiid~G~pq~t~~~~lk~~i~m~s~ee~i 143 (523)
...+.|+.|-+.+.-.+. +++...+.+|.--+.-++|||||.|...+|++++|-.-+.+.+.++.+
T Consensus 86 ~L~svL~~l~dal~llLr~nveKr~llEN~D~i~L~~DEiiD~GvILEtdp~~ia~rv~~~~~~~~~ 152 (175)
T KOG3343|consen 86 MLMSVLTCLFDALSLLLRKNVEKRELLENLDLIFLALDEIIDGGVILETDPNQIAQRVALRPTDEPL 152 (175)
T ss_pred HHHHHHHHHHHHHHHHHHhChhHHHHHhhhccceeehhhhccCceEEecCHHHHHHHhccCCCCcch
Confidence 999999999999998884 678888999944444459999999999999999999999998888754
No 14
>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=97.22 E-value=0.00095 Score=60.23 Aligned_cols=135 Identities=12% Similarity=0.105 Sum_probs=101.4
Q ss_pred eEEEEEEEcCCCCEEEEEcceecchHHHHHHH-------hhhchhhcC---CCCCcEEEeCCEEEEEEEcCCEEEEEEEc
Q 042402 2 VVLAASIVSKSGKILVSRQFVDMSRIRIEGLL-------AAFPKLVGT---GKQHTYVETENVRYVYQPIEALYLLLVTN 71 (523)
Q Consensus 2 ~v~s~~Il~~~G~~lisR~yr~~~r~~~e~~l-------~~F~~~i~~---~~~~p~i~~~~~~yvy~~~~~ly~v~~t~ 71 (523)
.|.|+.|+|++|+.+..|.|.+=-|++-+.++ ..|-+.+-. ..+..+....+.-.+|.++.++.|..+..
T Consensus 7 ~v~a~LilDsqGeriy~kyy~pph~~eg~~~vFnsvkkekefek~l~eKt~k~~~~Il~f~d~lV~~k~~~dv~~yiv~~ 86 (187)
T COG5541 7 DVEALLILDSQGERIYRKYYQPPHRSEGHQLVFNSVKKEKEFEKKLAEKTAKDRESILMFYDRLVMCKRLDDVLLYIVSP 86 (187)
T ss_pred eeeeeEEecCCccchhhhhcCCcccccccchhhcchhHHHHHHHHHHHHhhcCccceeeEcceeeeeeeehhEEEEEecc
Confidence 36789999999999998888832233211111 013333322 34567888888888999999988888888
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhcCC-CChhhHHhhHHHHHHhHHhHHhCCeecccCHHHHHHHhhc
Q 042402 72 KQSNILEDLETLRLLSKLVPEYSYS-LDEEGICKTAFELLFAFDEVISLGHKENVTVAQVKQYCEM 136 (523)
Q Consensus 72 ~n~n~~~~le~L~~l~~il~~y~g~-l~E~~I~~niyel~~~lDEiid~G~pq~t~~~~lk~~i~m 136 (523)
-+.|....-+.+..|...+.-.+.. -++..|.+|.-+++-+.||.||.|....|+++.|..-+.-
T Consensus 87 meeNE~~l~q~f~~ir~Al~li~k~~~dkr~v~enYDqivl~vdEtid~Gvilet~s~~ia~rv~K 152 (187)
T COG5541 87 MEENEPFLGQVFDEIRAALILIVKTPTDKRNVWENYDQIVLLVDETIDEGVILETKSDEIADRVPK 152 (187)
T ss_pred cccccHHHHHHHHHHHHHHHHHHcCCcchhhHHhhhceEEEeeehhcccceEeecChHHHHHhCCC
Confidence 8999999999999999988888865 5566699996666667999999999999998887755543
No 15
>PF03164 Mon1: Trafficking protein Mon1; InterPro: IPR004353 Members of this family have been called SAND proteins [] although these proteins do not contain a SAND domain. In Saccharomyces cerevisiae a protein complex of Mon1 and Ccz1 functions with the small GTPase Ypt7 to mediate vesicle trafficking to the vacuole [, ]. The Mon1/Ccz1 complex is conserved in eukaryotic evolution and members of this family (previously known as DUF254) are distant homologues to domains of known structure that assemble into cargo vesicle adapter (AP) complexes [, ].
Probab=92.03 E-value=1.4 Score=47.45 Aligned_cols=80 Identities=19% Similarity=0.223 Sum_probs=55.7
Q ss_pred EEEEEcCCCCEEEEEcceecchHHHHHHHhhhchhhcC----CCCCcEEEeCCEEEEEEEcCCEEEEEEEcCCCCHHHHH
Q 042402 5 AASIVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGT----GKQHTYVETENVRYVYQPIEALYLLLVTNKQSNILEDL 80 (523)
Q Consensus 5 s~~Il~~~G~~lisR~yr~~~r~~~e~~l~~F~~~i~~----~~~~p~i~~~~~~yvy~~~~~ly~v~~t~~n~n~~~~l 80 (523)
-+||++..||++-+|.=.+ ..+-.++..+..++.. ++.--.+..++.++++..+.-||+||+++.+.++....
T Consensus 13 h~fIlS~AGKPIysr~G~e---~~l~~~~g~~~aiiS~~~~~~d~l~~i~~~~~~ivfl~r~pl~lv~vS~~~e~~~~l~ 89 (415)
T PF03164_consen 13 HFFILSSAGKPIYSRYGDE---DKLSSLMGVIQAIISFFQSNGDELRSIRAGDHRIVFLNRGPLILVAVSKTGESESQLR 89 (415)
T ss_pred eEEEECCCCceeEEecCCh---HHHHHHHHHHHHHHHHHHhCCCcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCHHHHH
Confidence 3799999999999988323 3333444433333332 22334678899999999999999999999998866555
Q ss_pred HHHHHHH
Q 042402 81 ETLRLLS 87 (523)
Q Consensus 81 e~L~~l~ 87 (523)
..|..+.
T Consensus 90 ~qL~~ly 96 (415)
T PF03164_consen 90 KQLDYLY 96 (415)
T ss_pred HHHHHHH
Confidence 5555444
No 16
>PF08923 MAPKK1_Int: Mitogen-activated protein kinase kinase 1 interacting; InterPro: IPR015019 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry represents Mitogen-activated protein kinase kinase 1 interacting protein, which is a small subcellular adaptor protein required for MAPK signalling and ERK1/2 activation. The overall topology of this domain has a central five-stranded beta-sheet sandwiched between a two alpha-helix and a one alpha-helix layer []. ; PDB: 1VEU_A 1VET_A 1SKO_A 2ZL1_A 3CPT_A.
Probab=91.34 E-value=2.1 Score=37.80 Aligned_cols=91 Identities=16% Similarity=0.181 Sum_probs=63.8
Q ss_pred EEEEEEEcCCCCEEEEEcceecchHHH-HHHHhhhchhhcC------CCC-CcEEEeCCEEEEEEEcCCEEEEEEEcCCC
Q 042402 3 VLAASIVSKSGKILVSRQFVDMSRIRI-EGLLAAFPKLVGT------GKQ-HTYVETENVRYVYQPIEALYLLLVTNKQS 74 (523)
Q Consensus 3 v~s~~Il~~~G~~lisR~yr~~~r~~~-e~~l~~F~~~i~~------~~~-~p~i~~~~~~yvy~~~~~ly~v~~t~~n~ 74 (523)
+.+++|.|++|=+++.=..-+.+..+. ..++..|...... ++. .-+..++++..++.....+|+..+++.+.
T Consensus 17 l~~I~itDrDGvpi~~v~~~~~~~~~~~~~~~~tf~~a~~Q~~KL~lG~nk~ii~~Y~~~qvv~~~~~pl~it~ias~~a 96 (119)
T PF08923_consen 17 LQAIVITDRDGVPIAKVSSDSAPESAMRPSLLSTFAMAIDQASKLGLGKNKSIIAYYDSYQVVQFNKLPLYITFIASSNA 96 (119)
T ss_dssp EEEEEEEETTS-EEEEEE-TTS-GGGGSHHHHCCHHHHHHHHTTSSS-SEEEEEEEESSEEEEEEEETTEEEEEEEETTS
T ss_pred eEEEEEECCCCcEEEEecCCCCcchhhhhHHHHHHHHHhhcccccCCCCceEEEEEeCCEEEEEEeCCCeEEEEEecCCC
Confidence 679999999996666533334443333 3455555443332 333 34677899999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHHHhh
Q 042402 75 NILEDLETLRLLSKLVPEY 93 (523)
Q Consensus 75 n~~~~le~L~~l~~il~~y 93 (523)
|.-.++.+-..+..++.+.
T Consensus 97 N~G~il~l~~~L~~~l~~l 115 (119)
T PF08923_consen 97 NTGLILSLEEELAPILNEL 115 (119)
T ss_dssp -HHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHhHHHHHHHHHHH
Confidence 9999999999998888654
No 17
>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=87.51 E-value=6.6 Score=35.75 Aligned_cols=91 Identities=20% Similarity=0.332 Sum_probs=54.9
Q ss_pred EEEEEEEcCCCCEEEEEcce-ec----chHHHH--HH-------HhhhchhhcCCC-------CC--cEEEeCCEEE-EE
Q 042402 3 VLAASIVSKSGKILVSRQFV-DM----SRIRIE--GL-------LAAFPKLVGTGK-------QH--TYVETENVRY-VY 58 (523)
Q Consensus 3 v~s~~Il~~~G~~lisR~yr-~~----~r~~~e--~~-------l~~F~~~i~~~~-------~~--p~i~~~~~~y-vy 58 (523)
|.+++|+|+.|..+-.|.|. .. ++...+ .+ |.+|-..+.... .. ..++++.++. +|
T Consensus 1 IyslyI~nr~G~lIy~~~~~~~~~~~~~~~~~ne~~ll~g~l~sl~~i~~klsp~~~~~~~~~~~g~~~~~T~~yklh~~ 80 (142)
T PF04099_consen 1 IYSLYIFNRSGGLIYYREWNRSKNEGQPKLSSNEYKLLAGMLHSLKAIASKLSPVDSKPNEPGSSGFESFETDTYKLHCF 80 (142)
T ss_dssp EEEEEEE-TTS-EEEEEETSSSS--E-SSSCHHHHHHHHHHHHHHHHHHHHT-SSSSSS-SSS--SEEEEEESS-EEEEE
T ss_pred CeEEEEEeCCcceeeehhhCCCCccccCCCChhHHHHHHhhHHHHHHHHHHhCCCCcccccccceeEEEEEeCCEEEEEE
Confidence 67999999999999999998 43 111111 11 333444444310 11 2477778776 46
Q ss_pred EEcCCEEEEEEEcCCCCHHHHHHHHHHHHHHHHhhc
Q 042402 59 QPIEALYLLLVTNKQSNILEDLETLRLLSKLVPEYS 94 (523)
Q Consensus 59 ~~~~~ly~v~~t~~n~n~~~~le~L~~l~~il~~y~ 94 (523)
+..-|+-||++|+.+...+. =++++.+.++.-+|.
T Consensus 81 eT~TGlKFvl~td~~~~~~~-~~l~~~~~~lY~dyV 115 (142)
T PF04099_consen 81 ETPTGLKFVLITDPNVPSLR-DELLRIYYELYVDYV 115 (142)
T ss_dssp E-TTS-EEEEEE-TTCCHCH-HHHHHHHHHHHHHHH
T ss_pred EcCcCcEEEEEecCCCccHH-HHHHHHHHHHHHHHH
Confidence 88899999999999986543 336788888887775
No 18
>PF13774 Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3BW6_A 1H8M_A 3EGX_C 2NUP_C 3EGD_C 2NUT_C 3KYQ_A 1IFQ_B 2VX8_D ....
Probab=86.12 E-value=4.8 Score=32.69 Aligned_cols=50 Identities=14% Similarity=0.065 Sum_probs=43.5
Q ss_pred CcEEEeCCEEEEEEEcCCEEEEEEEcCCCCHHHHHHHHHHHHHHHHhhcC
Q 042402 46 HTYVETENVRYVYQPIEALYLLLVTNKQSNILEDLETLRLLSKLVPEYSY 95 (523)
Q Consensus 46 ~p~i~~~~~~yvy~~~~~ly~v~~t~~n~n~~~~le~L~~l~~il~~y~g 95 (523)
.-.++.+++.|-|...+++.++|+|+.....-..+.||..+.+-+..-++
T Consensus 16 k~s~~~~~~~fh~~~~~~i~~~citd~~~~~r~aF~fL~~i~~~F~~~~~ 65 (83)
T PF13774_consen 16 KMSYESGNYVFHYLVEDGIAYLCITDKSYPKRVAFAFLEEIKQEFIQTYG 65 (83)
T ss_dssp EEEEEETTEEEEEEEETTEEEEEEEETTS-HHHHHHHHHHHHHHHHHHCT
T ss_pred eEEEEECCEEEEEEEcCCeEEEEEEcCCCCcchHHHHHHHHHHHHHHHcC
Confidence 34678889888888899999999999999999999999999988887776
No 19
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=80.86 E-value=14 Score=32.22 Aligned_cols=91 Identities=20% Similarity=0.245 Sum_probs=55.9
Q ss_pred CeEEEEEEEcCCCCEEEEEcce-ecchHHHHHHH-------hhh--chhhcC-CCCCc--EEEeCC-EEEEEEEcCCEEE
Q 042402 1 MVVLAASIVSKSGKILVSRQFV-DMSRIRIEGLL-------AAF--PKLVGT-GKQHT--YVETEN-VRYVYQPIEALYL 66 (523)
Q Consensus 1 m~v~s~~Il~~~G~~lisR~yr-~~~r~~~e~~l-------~~F--~~~i~~-~~~~p--~i~~~~-~~yvy~~~~~ly~ 66 (523)
|.|-+++|+|+.|-.+..|.|. +-+.-....+| ..| ..++.. -...+ +++.+. +-++||..-++-|
T Consensus 1 mave~~~iINksGglifqref~~~et~lnsneyLiLastlhgV~aI~tq~~p~~gssg~~~l~~~~f~m~I~qT~TG~kF 80 (134)
T COG5122 1 MAVEQFFIINKSGGLIFQREFGEGETELNSNEYLILASTLHGVSAILTQTIPLPGSSGRLVLYFRNFVMTIFQTTTGTKF 80 (134)
T ss_pred CceeEEEEEecCCcEEEEEeccCCccccCcccEEEEeechhhhhhhhhhcccCCCCCceEEEEeccEEEEEEEecCCcEE
Confidence 7889999999999999999996 32211110100 000 001111 01112 345544 5568899999999
Q ss_pred EEEE-cCCCCHHHHHHHHHHHHHHHHhhc
Q 042402 67 LLVT-NKQSNILEDLETLRLLSKLVPEYS 94 (523)
Q Consensus 67 v~~t-~~n~n~~~~le~L~~l~~il~~y~ 94 (523)
|+++ ++.+|.+.- |+.+..+..||.
T Consensus 81 V~~~~k~t~na~~q---l~kiY~lYsdYV 106 (134)
T COG5122 81 VFVAEKRTVNALFQ---LQKIYSLYSDYV 106 (134)
T ss_pred EEEecCCchhHHHH---HHHHHHHHHHHh
Confidence 9999 555676654 667777777775
No 20
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=79.20 E-value=13 Score=35.44 Aligned_cols=78 Identities=21% Similarity=0.175 Sum_probs=60.8
Q ss_pred EEEEEEEcCCEEEEEEEcCCCCHHHHHHHHHHHHHHHHhhcCCCCh-hhHHhhHHHHHHhHHhHHhCCeecccCHHHHH
Q 042402 54 VRYVYQPIEALYLLLVTNKQSNILEDLETLRLLSKLVPEYSYSLDE-EGICKTAFELLFAFDEVISLGHKENVTVAQVK 131 (523)
Q Consensus 54 ~~yvy~~~~~ly~v~~t~~n~n~~~~le~L~~l~~il~~y~g~l~E-~~I~~niyel~~~lDEiid~G~pq~t~~~~lk 131 (523)
...++....++-|+++++...|.+++-.||+.|++.+.+.+..+.- ..+.-..-++.-+|+.++=.|--.-.|.+.+|
T Consensus 104 k~vvW~~v~~l~ftLVce~hEN~lLa~~~L~~~~~~l~~~~~~l~~~~e~l~k~d~i~aiL~~fLP~GQLLFlN~~~~k 182 (189)
T PF15001_consen 104 KIVVWLGVGSLCFTLVCEPHENRLLAENTLRLFIRHLLEHLKILSQPSEVLLKSDRILAILHRFLPHGQLLFLNHRFVK 182 (189)
T ss_pred cEEEeeccCCEEEEEEecCchhHHHHHHHHHHHHHHHHHHHHHhCcHHHhhhhHHHHHHHHHHhCCCCcEEEEcHHHHH
Confidence 4557889999999999999999999999999999999999854433 23333344444449999988988777776665
No 21
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=72.77 E-value=28 Score=31.16 Aligned_cols=86 Identities=16% Similarity=0.284 Sum_probs=49.8
Q ss_pred CeEEEEEEEcCCCCEEEEEccee-----cchHHHHHH-------HhhhchhhcCCC-CCcE--EEeCCEEEEE-EEcCCE
Q 042402 1 MVVLAASIVSKSGKILVSRQFVD-----MSRIRIEGL-------LAAFPKLVGTGK-QHTY--VETENVRYVY-QPIEAL 64 (523)
Q Consensus 1 m~v~s~~Il~~~G~~lisR~yr~-----~~r~~~e~~-------l~~F~~~i~~~~-~~p~--i~~~~~~yvy-~~~~~l 64 (523)
|+|.++.|+|+.|..|..|-|.. +++..-..+ +..|-..+..++ .-.| +.+..++.-| -.--+|
T Consensus 1 Mtiy~~yIFdR~g~Cl~y~EW~r~~~s~~~~eee~KL~yGmlFSlkS~v~Kls~~d~k~~f~sy~Ts~YklhfyeTptgl 80 (140)
T KOG3368|consen 1 MTIYNFYIFDRNGVCLFYREWNRTKQSGIPNEEEAKLMYGMLFSLKSFVSKLSPGDVKDGFLSYKTSKYKLHFYETPTGL 80 (140)
T ss_pred CeEEEEEEEcCCccEEEehhcccccccCCchhHHHHHHHHHHhhHHHHHHhcCCCCcccCeeEEeeceeEEEEEEcCCCc
Confidence 89999999999999998876652 222221122 233444444422 2234 3444444443 334589
Q ss_pred EEEEEEcCCCCHHHHHHHHHHHHH
Q 042402 65 YLLLVTNKQSNILEDLETLRLLSK 88 (523)
Q Consensus 65 y~v~~t~~n~n~~~~le~L~~l~~ 88 (523)
.||+.|+.+... +-+.||.|..
T Consensus 81 k~vl~Tdpk~~~--ir~vLq~IYs 102 (140)
T KOG3368|consen 81 KFVLNTDPKAGS--IRDVLQYIYS 102 (140)
T ss_pred EEEEecCCCccc--HHHHHHHHHH
Confidence 999999877533 2334555554
No 22
>KOG0997 consensus Uncharacterized conserved protein Sand [Function unknown]
Probab=70.12 E-value=29 Score=37.72 Aligned_cols=82 Identities=20% Similarity=0.231 Sum_probs=57.0
Q ss_pred EEEEcCCCCEEEEEcce-ecc---hHHHHHHHhhhchhhcC-CCCCcEEEeCCEEEEEEEcCCEEEEEEEcCCCCHHH-H
Q 042402 6 ASIVSKSGKILVSRQFV-DMS---RIRIEGLLAAFPKLVGT-GKQHTYVETENVRYVYQPIEALYLLLVTNKQSNILE-D 79 (523)
Q Consensus 6 ~~Il~~~G~~lisR~yr-~~~---r~~~e~~l~~F~~~i~~-~~~~p~i~~~~~~yvy~~~~~ly~v~~t~~n~n~~~-~ 79 (523)
+||++..|+++.+|.=. +.. -..+..++.-| .. +..-..+...|.++++...+-|++||.++.+..+-+ .
T Consensus 120 ifilseaGKPiyS~~gs~e~l~stmGv~~alISf~----q~~~~~i~si~a~g~k~vfl~kspl~LvA~s~t~~Sa~qL~ 195 (523)
T KOG0997|consen 120 IFILSEAGKPIYSRHGSDEALSSTMGVMQALISFF----QVSGLAITSIHAFGNKLVFLQKSPLLLVAVSRTSQSAAQLL 195 (523)
T ss_pred EEEEecCCCceeeecCcHHHHHHHHHHHHHHHHHH----hhCCceEEEEEecCceEEEEecCcEEEEEEcccccCHHHHH
Confidence 79999999999999877 211 23333333322 22 334467888999999999999999999998866543 4
Q ss_pred HHHHHHHHHHHH
Q 042402 80 LETLRLLSKLVP 91 (523)
Q Consensus 80 le~L~~l~~il~ 91 (523)
.+++....+|+.
T Consensus 196 ~qL~~ly~QIlS 207 (523)
T KOG0997|consen 196 QQLLLLYCQILS 207 (523)
T ss_pred HHHHHHHHHHHH
Confidence 445555556664
No 23
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=70.11 E-value=46 Score=31.30 Aligned_cols=45 Identities=16% Similarity=0.347 Sum_probs=35.1
Q ss_pred EEEeCCEE-EEEEEcCCEEEEEEEcCCCCHHHHHHHHHHHHHHHHhhc
Q 042402 48 YVETENVR-YVYQPIEALYLLLVTNKQSNILEDLETLRLLSKLVPEYS 94 (523)
Q Consensus 48 ~i~~~~~~-yvy~~~~~ly~v~~t~~n~n~~~~le~L~~l~~il~~y~ 94 (523)
+++.+..+ ++||.+-++=||++++...+.+. .+|+++.++..||.
T Consensus 125 ~LetdtF~l~~~QTlTG~KFVvis~~~~~~aD--~lLrKiYelYsDyv 170 (199)
T KOG3369|consen 125 VLETDTFTLHIFQTLTGTKFVVIAEPGTQGAD--SLLRKIYELYSDYV 170 (199)
T ss_pred EEEeccEEEEEEEccCCcEEEEEecCCchhHH--HHHHHHHHHHHHHh
Confidence 46666644 57999999999999998875443 36888998888885
No 24
>KOG0861 consensus SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=63.80 E-value=31 Score=32.48 Aligned_cols=91 Identities=21% Similarity=0.347 Sum_probs=57.2
Q ss_pred CeEEEEEEEcCCCC-EEEEEcceecc------hHHHHHHHhhhchhhcC--C-CCCcEEEeCC-EEEEEEEcCCEEEEEE
Q 042402 1 MVVLAASIVSKSGK-ILVSRQFVDMS------RIRIEGLLAAFPKLVGT--G-KQHTYVETEN-VRYVYQPIEALYLLLV 69 (523)
Q Consensus 1 m~v~s~~Il~~~G~-~lisR~yr~~~------r~~~e~~l~~F~~~i~~--~-~~~p~i~~~~-~~yvy~~~~~ly~v~~ 69 (523)
|-|.|+.++...+. +.+-+.=.|++ |+.+..++.-|-+.+-. + .+---+..+. ...+|.+-++|--|++
T Consensus 1 Mki~sl~V~~~~~~~~~ll~~a~dls~FsfFqRssV~Efm~F~sktvaeRt~~g~rqsvk~~~Y~~h~yvrndgL~~V~~ 80 (198)
T KOG0861|consen 1 MKIYSLSVLHKGTSDVKLLKTASDLSSFSFFQRSSVQEFMTFISKTVAERTGPGQRQSVKHEEYLVHVYVRNDGLCGVLI 80 (198)
T ss_pred CceEEEEEEeeCCcchhhhhhhcccccccceeeccHHHHHHHHHHHHHHhcCcccccccccceeEEEEEEecCCeeEEEE
Confidence 77899999998543 33322222333 77888766544444443 1 1111234444 3457888889999999
Q ss_pred EcCCCCHHHHHHHHHHHHHHHHhhc
Q 042402 70 TNKQSNILEDLETLRLLSKLVPEYS 94 (523)
Q Consensus 70 t~~n~n~~~~le~L~~l~~il~~y~ 94 (523)
++.+-....++.+|. +++++|.
T Consensus 81 ~D~eYP~rvA~tLL~---kvld~~~ 102 (198)
T KOG0861|consen 81 ADDEYPVRVAFTLLN---KVLDEFT 102 (198)
T ss_pred ecCcCchhHHHHHHH---HHHHHHh
Confidence 998888777777665 4666664
No 25
>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=63.16 E-value=27 Score=28.70 Aligned_cols=42 Identities=29% Similarity=0.314 Sum_probs=28.9
Q ss_pred ceeeeEEEEecCCCCCCCCeEEeecceEEEECCCCEEEEEEceecC
Q 042402 413 FDLRNVVISVPLPALREAPSVRQIDGEWRYDSRNSVLEWTILLIDN 458 (523)
Q Consensus 413 ~~~~~V~V~iPlP~~~~~~~~~~~~G~~~~~~~~~~l~W~I~~i~~ 458 (523)
..+-||+|+=.||- .+++.+++-...- ..++.|+|+|+.+..
T Consensus 42 ~DcvnVviTqqLPc---e~eFV~SdPettp-~~D~kLVW~Ig~l~~ 83 (95)
T PF03504_consen 42 KDCVNVVITQQLPC---EVEFVRSDPETTP-TPDGKLVWKIGRLGQ 83 (95)
T ss_pred cceeEEEEeecCCc---ceEEEecCCcccc-CCCCEEEEEeccccC
Confidence 34788889888886 3455544443331 266799999999975
No 26
>PF00235 Profilin: Profilin; InterPro: IPR002097 Profilin is a small eukaryotic protein that binds to monomeric actin (G-actin) in a 1:1 ratio thus preventing the polymerisation of actin into filaments (F-actin). It can also in certain circumstance promote actin polymerisation. Profilin also binds to polyphosphoinositides such as PIP2. Overall sequence similarity among profilin from organisms which belong to different phyla (ranging from fungi to mammals) is low, but the N-terminal region is relatively well conserved. That region is thought to be involved in the binding to actin. A protein structurally similar to profilin is present in the genome of Variola virus and Vaccinia virus (gene A42R). Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Ara t 8, Bet v 2, Cyn d 12, Hel a 2, Mer a 1 and Phl p 11.; GO: 0003779 actin binding, 0007010 cytoskeleton organization, 0015629 actin cytoskeleton; PDB: 1ACF_A 3NEC_C 2V8F_B 2V8C_A 2VK3_A 2JKF_A 2JKG_A 1F2K_B 2ACG_A 1YPR_B ....
Probab=61.16 E-value=70 Score=27.71 Aligned_cols=86 Identities=12% Similarity=0.185 Sum_probs=56.7
Q ss_pred EEEEEEEcCCCCEEEEEc-ceecchHHHHHHHhhhchhhcCCCCCcEEEeCCEEEEEEEc-------------------C
Q 042402 3 VLAASIVSKSGKILVSRQ-FVDMSRIRIEGLLAAFPKLVGTGKQHTYVETENVRYVYQPI-------------------E 62 (523)
Q Consensus 3 v~s~~Il~~~G~~lisR~-yr~~~r~~~e~~l~~F~~~i~~~~~~p~i~~~~~~yvy~~~-------------------~ 62 (523)
+.+++|++.+|.+..+.. |..++...+..++..|-.. ......-|.++|.+|...+. +
T Consensus 16 ~~~aaI~~~dG~vwA~s~~f~~~~~~E~~~i~~~f~~~--~~~~~~gi~l~G~kY~~~~~d~~~i~~k~~~~G~~i~kt~ 93 (121)
T PF00235_consen 16 ITKAAIIGSDGSVWASSPGFSNISPEEAKAIIKAFNNP--SKFPSNGITLGGKKYIVLRADDNSIYGKKGKGGIIIVKTK 93 (121)
T ss_dssp ESEEEEEETTSSEEEEETTGGGCSHHHHHHHHHHHHSS--SHHHHH-EEETTEEEEEEEEETTEEEEEETTEEEEEEECS
T ss_pred EeEEEEEcCCCCEEEecCCCCCCCHHHHHHHHHHhcCc--hhcccCCeEEcCcEeEEEecCCceEEeeCCCCcEEEEECC
Confidence 457899999998888665 4366767776766655442 00112346666666655443 4
Q ss_pred CEEEEEEEcCCCCHHHHHHHHHHHHHHH
Q 042402 63 ALYLLLVTNKQSNILEDLETLRLLSKLV 90 (523)
Q Consensus 63 ~ly~v~~t~~n~n~~~~le~L~~l~~il 90 (523)
..++|+..+.+.++-...+...+|++.|
T Consensus 94 ~~ivIg~y~~~~~~~~~~~~v~~lA~yL 121 (121)
T PF00235_consen 94 QAIVIGMYDESIQPGNCNKAVEKLADYL 121 (121)
T ss_dssp SEEEEEEEETTSTHHHHHHHHHHHHHHH
T ss_pred CEEEEEEeCCCCCHHHHHHHHHHHHhhC
Confidence 4677788888888888888888887654
No 27
>PF09201 SRX: SRX; InterPro: IPR015284 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. This entry represents a homologue of the alpha subunit of the SR receptor. Members of this entry consist of a central six-stranded anti-parallel beta-sheet sandwiched by helix alpha1 on one side and helices alpha2-alpha4 on the other. They interact with the small GTPase SR-beta, forming a complex that matches a class of small G protein-effector complexes, including Rap-Raf, Ras-PI3K(gamma), Ras-RalGDS, and Arl2-PDE(delta) []. ; PDB: 1NRJ_A.
Probab=52.30 E-value=34 Score=30.95 Aligned_cols=67 Identities=15% Similarity=0.249 Sum_probs=38.1
Q ss_pred EEEEEEcCCCCEEEEEcceecchHHHHHHHhhhchhhcCC--------CCCcEEEe-------CCEEEEE--EEcCCEEE
Q 042402 4 LAASIVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGTG--------KQHTYVET-------ENVRYVY--QPIEALYL 66 (523)
Q Consensus 4 ~s~~Il~~~G~~lisR~yr~~~r~~~e~~l~~F~~~i~~~--------~~~p~i~~-------~~~~yvy--~~~~~ly~ 66 (523)
=.++|++.+|++|. +|-...|.-.|..+.+|...+.+. ....+..+ ++++++| -+...|||
T Consensus 3 dQlaIFTpqGqvLy--qyN~~gKKFsE~QiN~FIs~lItsP~~~~e~~~~~k~~~i~s~~~~~~~f~~mfh~sKQPeLy~ 80 (148)
T PF09201_consen 3 DQLAIFTPQGQVLY--QYNCLGKKFSETQINAFISHLITSPVTKKEDSSKSKFLTISSEKKNSRSFSAMFHISKQPELYY 80 (148)
T ss_dssp -EEEEE-TT-BEEE--EEETTS----HHHHHHHHHHHHHS---GGGTT--EEEEE-----------EEEEEEETTTTEEE
T ss_pred ceeEEeccCceEEE--EecccchHHHHHHHHHHHHHHhcCCCcccCCCcceeeEEecccccCCCChheeeeecCCCcEEE
Confidence 35789999999986 355666667777788888766641 11234433 4777776 34568999
Q ss_pred EEEEcC
Q 042402 67 LLVTNK 72 (523)
Q Consensus 67 v~~t~~ 72 (523)
|++--.
T Consensus 81 VvTyae 86 (148)
T PF09201_consen 81 VVTYAE 86 (148)
T ss_dssp EEEESS
T ss_pred EEEecc
Confidence 998865
No 28
>KOG2265 consensus Nuclear distribution protein NUDC [Signal transduction mechanisms]
Probab=32.72 E-value=49 Score=31.16 Aligned_cols=41 Identities=29% Similarity=0.485 Sum_probs=25.1
Q ss_pred eeeeEEEEecCCCCC-CCCeEEe-----------------ecceEEEECCCCEEEEEEc
Q 042402 414 DLRNVVISVPLPALR-EAPSVRQ-----------------IDGEWRYDSRNSVLEWTIL 454 (523)
Q Consensus 414 ~~~~V~V~iPlP~~~-~~~~~~~-----------------~~G~~~~~~~~~~l~W~I~ 454 (523)
++++|.|.||+|+++ .+-.+.+ .+|...+........|+|.
T Consensus 26 tL~EV~i~i~vp~~~~ksk~v~~~Iq~~hI~V~~kg~~~ildG~L~~~vk~des~WtiE 84 (179)
T KOG2265|consen 26 TLEEVEIQIPVPPGTAKSKDVHCSIQSKHIKVGLKGQPPILDGELSHSVKVDESTWTIE 84 (179)
T ss_pred ehhheEEEeecCCCCcccceEEEEeeeeEEEEecCCCCceecCccccccccccceEEec
Confidence 577888888888866 3322221 2455555556667778874
No 29
>KOG0592 consensus 3-phosphoinositide-dependent protein kinase (PDK1) [Signal transduction mechanisms]
Probab=32.42 E-value=1.7e+02 Score=32.63 Aligned_cols=65 Identities=26% Similarity=0.311 Sum_probs=47.4
Q ss_pred CCcEEEeCCEEEEEEEcCCEEEEEEEcCCCCHHHHHHHHHHHHHHHHhhcCCCChhhHHhhHHHHHHhHHhHHhCCee
Q 042402 45 QHTYVETENVRYVYQPIEALYLLLVTNKQSNILEDLETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISLGHK 122 (523)
Q Consensus 45 ~~p~i~~~~~~yvy~~~~~ly~v~~t~~n~n~~~~le~L~~l~~il~~y~g~l~E~~I~~niyel~~~lDEiid~G~p 122 (523)
.||.|.. ..|.+|....||||+---.|.. .|++|+ .| |.++|..-|.-.=||+.+||-|=+.|..
T Consensus 132 ~hPgivk--Ly~TFQD~~sLYFvLe~A~nGd---ll~~i~-------K~-Gsfde~caR~YAAeIldAleylH~~GII 196 (604)
T KOG0592|consen 132 GHPGIVK--LYFTFQDEESLYFVLEYAPNGD---LLDLIK-------KY-GSFDETCARFYAAEILDALEYLHSNGII 196 (604)
T ss_pred CCCCeEE--EEEEeecccceEEEEEecCCCc---HHHHHH-------Hh-CcchHHHHHHHHHHHHHHHHHHHhcCce
Confidence 3554433 5777899999999998877753 223333 33 7899999888888998889988887754
No 30
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=31.88 E-value=4.8e+02 Score=25.25 Aligned_cols=91 Identities=9% Similarity=0.057 Sum_probs=57.8
Q ss_pred CeEEEEEEEcCCCCEEEEEcce-ecch-HHHHHHHhhhchhhcCC-CCCcEEEeCCEEEEEEEcCCEEEEEEEcCCCCHH
Q 042402 1 MVVLAASIVSKSGKILVSRQFV-DMSR-IRIEGLLAAFPKLVGTG-KQHTYVETENVRYVYQPIEALYLLLVTNKQSNIL 77 (523)
Q Consensus 1 m~v~s~~Il~~~G~~lisR~yr-~~~r-~~~e~~l~~F~~~i~~~-~~~p~i~~~~~~yvy~~~~~ly~v~~t~~n~n~~ 77 (523)
|.|+=+++ .+|-++++..-- .-.- +..+.+|. .+..+ ..+=-...+++.|-|...|++-++|+++...---
T Consensus 1 m~iiYs~V--ARGTvvLaeft~~~gNf~sva~qiL~----klp~~~n~k~tYs~d~y~Fh~l~~dg~tylcvadds~gR~ 74 (217)
T KOG0859|consen 1 MSIIYSFV--ARGTVILAEFTEFSGNFSSIAAQILQ----KLPSSSNSKFTYSCDGYTFHYLVEDGLTYLCVADDSAGRQ 74 (217)
T ss_pred CceeEEEE--ecceEEEEeeeeccCCHHHHHHHHHH----hCCCCCCCceEEecCCeEEEEEEeCCeEEEEEEecccccc
Confidence 34443443 368788877544 2111 22333222 23332 2233467799999999999999999998776556
Q ss_pred HHHHHHHHHHHHHHhhcCCC
Q 042402 78 EDLETLRLLSKLVPEYSYSL 97 (523)
Q Consensus 78 ~~le~L~~l~~il~~y~g~l 97 (523)
.-+.||.++.+-+..-+|.-
T Consensus 75 ipfaFLe~Ik~~F~k~YG~~ 94 (217)
T KOG0859|consen 75 IPFAFLERIKEDFKKRYGGG 94 (217)
T ss_pred ccHHHHHHHHHHHHHHhccc
Confidence 67788999987777666644
No 31
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.65 E-value=3.2e+02 Score=26.75 Aligned_cols=50 Identities=12% Similarity=0.036 Sum_probs=44.2
Q ss_pred EEEeCCEEEEEEEcCCEEEEEEEcCCCCHHHHHHHHHHHHHHHHhhcCCC
Q 042402 48 YVETENVRYVYQPIEALYLLLVTNKQSNILEDLETLRLLSKLVPEYSYSL 97 (523)
Q Consensus 48 ~i~~~~~~yvy~~~~~ly~v~~t~~n~n~~~~le~L~~l~~il~~y~g~l 97 (523)
-+|.+.+.|-|.-..++.++++++++..--+++.+|.-+.+=+..-+|.-
T Consensus 53 Sietg~f~fHfli~~~Vcylvicd~~yP~kLAF~YLedL~~EF~~~~~~~ 102 (216)
T KOG0862|consen 53 SIETGPFVFHFLIESGVCYLVICDKSYPRKLAFSYLEDLAQEFDKSYGKN 102 (216)
T ss_pred ccccCCeEEEEEecCCEEEEEEecCCCcHHHHHHHHHHHHHHHHHhcccc
Confidence 47888899999999999999999999999999999999998888777643
No 32
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.53 E-value=4.3e+02 Score=29.23 Aligned_cols=108 Identities=20% Similarity=0.188 Sum_probs=72.3
Q ss_pred EEEEEcCCCCEEEEEcceecchHHHHHHHhhhchhhcC---CCCCcEEEeCCEEEEEEEcC--CEEEEEEEcCCCCHHHH
Q 042402 5 AASIVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGT---GKQHTYVETENVRYVYQPIE--ALYLLLVTNKQSNILED 79 (523)
Q Consensus 5 s~~Il~~~G~~lisR~yr~~~r~~~e~~l~~F~~~i~~---~~~~p~i~~~~~~yvy~~~~--~ly~v~~t~~n~n~~~~ 79 (523)
.++|+++.|-+|-..+=.... - ...+..|++.+.. +.... +..+.++.=|+-.+ +|.||++-..--+-..+
T Consensus 4 ~faIFtkgG~vLw~~~~~~~~--~-~~~in~lI~~~ll~er~~~~~-~~~~~yTlk~q~~N~~~lvfvvvfqki~~L~yv 79 (587)
T KOG0781|consen 4 QFAIFTKGGLVLWCYQEVGDN--L-KGPINALIRSVLLSERGGVNS-FTFEAYTLKYQLDNQYSLVFVVVFQKILTLTYV 79 (587)
T ss_pred eeeeecCCcEEEEEecccchh--c-cchHHHHHHHHHHHhhcCccc-CchhheeEeeeecCCccEEEEEEEeccchhhhH
Confidence 478999999887665544211 1 1133345554432 11112 56666666677666 57778887777788888
Q ss_pred HHHHHHHHHHHHhhcCCCChhhHHhhHHHHHHhHHhHHhC
Q 042402 80 LETLRLLSKLVPEYSYSLDEEGICKTAFELLFAFDEVISL 119 (523)
Q Consensus 80 le~L~~l~~il~~y~g~l~E~~I~~niyel~~~lDEiid~ 119 (523)
-.+|....+++.+-|....-..++.|.+++ ..|++..
T Consensus 80 ~~ll~~v~~~f~e~~~~~~~~~l~~n~~~~---~~e~lk~ 116 (587)
T KOG0781|consen 80 DKLLNDVLNLFREKYDTQSALSLLNNTFDF---QEELLKL 116 (587)
T ss_pred HHHHHHHHHHHHHHhccchHHHhhhhhHHH---HHHHHHH
Confidence 888888888888888777777788887777 7777764
No 33
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=28.43 E-value=85 Score=26.38 Aligned_cols=16 Identities=25% Similarity=0.137 Sum_probs=12.8
Q ss_pred HHhHHhHHhCCeeccc
Q 042402 110 LFAFDEVISLGHKENV 125 (523)
Q Consensus 110 ~~~lDEiid~G~pq~t 125 (523)
..+||++++-|+...|
T Consensus 83 ~~al~~L~~eG~IYsT 98 (102)
T PF08784_consen 83 RKALDFLSNEGHIYST 98 (102)
T ss_dssp HHHHHHHHHTTSEEES
T ss_pred HHHHHHHHhCCeEecc
Confidence 4449999999998876
No 34
>PF03259 Robl_LC7: Roadblock/LC7 domain; InterPro: IPR004942 This family includes proteins that are about 100 amino acids long and have been shown to be related []. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions []. This family also includes Golgi-associated MP1 adapter protein (Q9Y2Q5 from SWISSPROT) and MglB from Myxococcus xanthus (Q50883 from SWISSPROT), a protein involved in gliding motility []. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role.; PDB: 2B95_B 1Z09_A 2E8J_B 2HZ5_B 3KYE_A 2ZL1_B 1SKO_B 3CPT_B 1VEU_B 1VET_B ....
Probab=27.43 E-value=2.3e+02 Score=22.54 Aligned_cols=66 Identities=21% Similarity=0.350 Sum_probs=36.8
Q ss_pred EEEEEEEcCCCCEEEEEcceecchHHHHHHHhhhchhhcC-----C--C-CCcEEEeCCEEEEEEEcCC-EEEEE
Q 042402 3 VLAASIVSKSGKILVSRQFVDMSRIRIEGLLAAFPKLVGT-----G--K-QHTYVETENVRYVYQPIEA-LYLLL 68 (523)
Q Consensus 3 v~s~~Il~~~G~~lisR~yr~~~r~~~e~~l~~F~~~i~~-----~--~-~~p~i~~~~~~yvy~~~~~-ly~v~ 68 (523)
|.++.|+|++|.++-+....+..-..+-...+.++..... + . ..-+++.+....+..+.++ .++++
T Consensus 15 v~~~~l~~~dG~~i~~~~~~~~~~~~~aa~~a~~~~~~~~~~~~l~~~~~~~v~i~~~~~~i~i~~~~~~~~L~v 89 (91)
T PF03259_consen 15 VRGAVLVDKDGLVIASSGIDDDDAEKLAAMAASLLAAAEKLAKELGEGELEQVRIETEKGEIIITPVGDFYLLVV 89 (91)
T ss_dssp EEEEEEEETTSEEEEETSSSHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEEEEEESSEEEEEEECSTCEEEEE
T ss_pred eeEEEEEcCCCCEEEEecCCcccHHHHHHHHHHHHHHHHHHHHHhCCCCcEEEEEEECCCEEEEEEcCCCEEEEE
Confidence 5789999999988887233222212222222333322221 2 1 2246788887877788877 44444
No 35
>KOG0582 consensus Ste20-like serine/threonine protein kinase [Signal transduction mechanisms]
Probab=23.26 E-value=8.3e+02 Score=26.87 Aligned_cols=100 Identities=16% Similarity=0.189 Sum_probs=61.8
Q ss_pred EEEEcCCCCEEEEEcce-ecchHHHHHHHhhhchhhcC---CCCCcEEEeCCEEEEEEEcCCEEEEEEEcCCCCHHHHHH
Q 042402 6 ASIVSKSGKILVSRQFV-DMSRIRIEGLLAAFPKLVGT---GKQHTYVETENVRYVYQPIEALYLLLVTNKQSNILEDLE 81 (523)
Q Consensus 6 ~~Il~~~G~~lisR~yr-~~~r~~~e~~l~~F~~~i~~---~~~~p~i~~~~~~yvy~~~~~ly~v~~t~~n~n~~~~le 81 (523)
.+++-+.|++.--|.+- +=-+..++. ..+.+.. -..|+++.. +..++-.+.||+|+---....
T Consensus 44 ~A~c~p~~e~VAIK~inLEkc~~~ld~----l~kE~~~msl~~HPNIv~~---~~sFvv~~~LWvVmpfMa~GS------ 110 (516)
T KOG0582|consen 44 LARCIPTNEVVAIKIINLEKCNNDLDA----LRKEVQTMSLIDHPNIVTY---HCSFVVDSELWVVMPFMAGGS------ 110 (516)
T ss_pred eeeecccCCEEEEEEeehhhhhhhHHH----HHHHHHHhhhcCCCCcceE---EEEEEecceeEEeehhhcCCc------
Confidence 44566666776666554 322233333 5555554 123346654 556677789999976543322
Q ss_pred HHHHHHHHHHhhc-CCCChhhHHhhHHHHHHhHHhHHhCCee
Q 042402 82 TLRLLSKLVPEYS-YSLDEEGICKTAFELLFAFDEVISLGHK 122 (523)
Q Consensus 82 ~L~~l~~il~~y~-g~l~E~~I~~niyel~~~lDEiid~G~p 122 (523)
+.++++.|| .+++|..|..=..|+|.+||=+=..||.
T Consensus 111 ----~ldIik~~~~~Gl~E~~Ia~iLre~LkaL~YLH~~G~I 148 (516)
T KOG0582|consen 111 ----LLDIIKTYYPDGLEEASIATILREVLKALDYLHQNGHI 148 (516)
T ss_pred ----HHHHHHHHccccccHHHHHHHHHHHHHHHHHHHhcCce
Confidence 335677788 4688888876689998888876666654
No 36
>PF04086 SRP-alpha_N: Signal recognition particle, alpha subunit, N-terminal; InterPro: IPR007222 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. This entry represents the alpha subunit of the SR receptor.; GO: 0003924 GTPase activity, 0005047 signal recognition particle binding, 0005525 GTP binding, 0006184 GTP catabolic process, 0006886 intracellular protein transport, 0005785 signal recognition particle receptor complex; PDB: 2FH5_A 2GO5_1.
Probab=22.44 E-value=1.2e+02 Score=30.41 Aligned_cols=51 Identities=12% Similarity=0.007 Sum_probs=31.5
Q ss_pred CCcEEEeCCEEEEEEEcC--CEEEEEEEcCCCCHHHHHHHHHHHHHHHHhhcC
Q 042402 45 QHTYVETENVRYVYQPIE--ALYLLLVTNKQSNILEDLETLRLLSKLVPEYSY 95 (523)
Q Consensus 45 ~~p~i~~~~~~yvy~~~~--~ly~v~~t~~n~n~~~~le~L~~l~~il~~y~g 95 (523)
..+.+.++++++=|.-.| +|.||++-.+--..+.+=+||..+...+.+.|+
T Consensus 18 ~~~~~~~d~y~lkw~~~Ne~~LvfVvvYq~il~l~yvd~LL~~v~~~F~~~y~ 70 (279)
T PF04086_consen 18 GNSSFTYDNYTLKWTLDNELGLVFVVVYQKILQLTYVDKLLDDVKKEFVKLYK 70 (279)
T ss_dssp ----------EEEEEEETTTTEEEEEEES-GGGHHHHHHHHHHHHHHHHHHTH
T ss_pred CCCceeEcCEEEEEEEeccCCEEEeeeecccccchHHHHHHHHHHHHHHHHHh
Confidence 445678888888887777 599999998777777777788777777777664
Done!