Query 044308
Match_columns 645
No_of_seqs 48 out of 50
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 13:23:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044308.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044308hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10291 muHD: Muniscin C-term 100.0 3E-46 6.4E-51 371.1 19.2 231 408-645 4-257 (257)
2 KOG2398 Predicted proline-seri 100.0 3.3E-33 7.2E-38 306.1 -3.2 599 23-645 1-611 (611)
3 PF00928 Adap_comp_sub: Adapto 99.5 1.7E-12 3.7E-17 126.3 18.6 226 408-644 16-260 (262)
4 KOG2635 Medium subunit of clat 98.9 3.8E-06 8.3E-11 91.2 30.9 167 465-643 333-510 (512)
5 KOG0937 Adaptor complexes medi 98.5 6.5E-06 1.4E-10 89.0 17.4 206 409-624 171-397 (424)
6 PF01217 Clat_adaptor_s: Clath 97.1 0.0032 7E-08 57.5 9.3 71 92-168 52-122 (141)
7 KOG0938 Adaptor complexes medi 96.1 0.63 1.4E-05 50.7 19.2 226 400-642 176-443 (446)
8 KOG2398 Predicted proline-seri 93.1 0.026 5.7E-07 64.3 -0.1 51 407-463 551-611 (611)
9 KOG2740 Clathrin-associated pr 92.1 9.6 0.00021 42.2 17.3 218 410-642 183-414 (418)
10 KOG2677 Stoned B synaptic vesi 75.9 11 0.00024 44.5 8.5 137 486-624 685-868 (922)
11 PF02883 Alpha_adaptinC2: Adap 56.1 1.4E+02 0.003 26.3 9.8 89 506-612 11-103 (115)
12 TIGR02385 RelE_StbE addiction 51.6 28 0.0006 28.4 4.4 38 74-111 42-82 (88)
13 TIGR02572 LcrR type III secret 47.4 63 0.0014 31.7 6.6 63 91-153 33-107 (139)
14 smart00809 Alpha_adaptinC2 Ada 37.8 2.6E+02 0.0057 24.0 10.8 86 506-612 7-92 (104)
15 PF11353 DUF3153: Protein of u 34.1 1.2E+02 0.0026 30.2 6.6 46 536-586 134-179 (209)
16 PF10686 DUF2493: Protein of u 33.6 28 0.0006 29.8 1.8 31 130-168 2-32 (71)
17 PF06437 ISN1: IMP-specific 5' 27.3 42 0.0009 37.6 2.3 21 144-164 50-70 (408)
18 PF05016 Plasmid_stabil: Plasm 26.3 1.1E+02 0.0024 24.9 4.1 19 94-112 64-85 (90)
19 PF09621 LcrR: Type III secret 24.4 4.5E+02 0.0097 25.9 8.3 63 91-153 33-107 (139)
No 1
>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=100.00 E-value=3e-46 Score=371.10 Aligned_cols=231 Identities=28% Similarity=0.420 Sum_probs=168.6
Q ss_pred ceEEEEEEEEEEecceeEEEeeeeEEEEEecCCCCCCCCCceeEEEEEeccchhhhhcccccccc--cCCCcceEEecCC
Q 044308 408 EMYIVEQVNAEFRESLLARVGLMGAVYLRTMPKKTSGDDKDTEFSFRVEGTSAVKRFAVQSSKVS--SLGDGMFHVRTAP 485 (645)
Q Consensus 408 ~~afTE~inA~FkGs~LvRVG~~GiVrvfT~~P~pa~~~k~~vlSFRL~~tS~Vk~F~pns~l~~--S~~tgdF~vr~~a 485 (645)
.++|+|+|||+|||+++.|+.+.|.|.+--.++......+...++|||+|++++|+|+||..+++ +...++|++....
T Consensus 4 ~asi~E~VnA~Fk~g~~~~v~v~GEv~ls~~~~~~~~~~~~~~l~~rl~n~~~le~i~pN~~~v~~~~~~~~~f~~n~~~ 83 (257)
T PF10291_consen 4 NASITETVNAYFKGGQLSKVKVTGEVALSYPAGISSSLTSPPPLSFRLNNFSRLEKIAPNPQFVSSSSQSDGEFWLNMSA 83 (257)
T ss_dssp EEEEEEEEEEEEETTEEEEEEEEEEEEEEEE--SSS-----SEEEEEEETGGGEEEEEE-TTTE--EEEETTEEEE-TTT
T ss_pred eEEEEEEEEEEEECCcEEEEEEEEEEEEecCCChhhcccCCCcEEEEEcCcchhceeecCHhHeecCCCCCCcEEEehHH
Confidence 57999999999999999999999999988555443321224589999999999999999999994 4577889997654
Q ss_pred --CCCCcceEEeeeCCCC---CCCCcEEEEEEeecCceEEEEEEEEeCC-CC--CCCccceEEEeecCCC-CCccccccc
Q 044308 486 --SDEPIPILRYSLLPRL---TPLPLRVRLIKRHSGTLLSVMVQYVSNP-DL--PMPLNDVTFSLKLPVD-PTLLKVSPK 556 (645)
Q Consensus 486 --SyynVpILKYql~pg~---~p~PL~lr~~wk~~~tlt~V~VdY~yNP-~l--p~PLtnVq~iL~VPvd-~tlLqs~P~ 556 (645)
++-....|||||.... ..+||+++.+|||+++.++|+|+|+||| .. +.+|+||+|+++|..+ .+++|++|.
T Consensus 84 l~~~~~~~alKYqv~~~~~~~~~~Pl~l~~~Wk~e~~~tsl~l~Y~~Np~~~~~~~~L~nv~~~v~l~g~~~ts~~skP~ 163 (257)
T PF10291_consen 84 LTSHLPKQALKYQVHSDPSNLSSVPLILKPVWKCEPSQTSLILDYKLNPDAFASPVPLENVVFSVPLDGGRATSAQSKPQ 163 (257)
T ss_dssp TBT-E-EEEEEEEEES--------SEEEEEEEEE-SSEEEEEEEEEE-TTT--E-EEEEEEEEEEEB-SS-EEEEEESSS
T ss_pred hhhhhhhceEEEEEeccccccCCCCeEEEeEEEeCCceEEEEEEEEeChhhccccceeeeEEEEEEcCCccccccccCCC
Confidence 4444578999998744 9999999999999999999999999999 44 4589999999999888 779999999
Q ss_pred cccccccceeeEEccCCCCCCCC--ceEEEEeecCCCCCCCCCccceEEEEEEeec-CCccccceeeeec---------C
Q 044308 557 AVLNRSDRELKWIVPEIPVKGAP--GKLRVRMPVDSSEEDGGEEIDVVCHVKFASQ-GMLSLSGVCLRPA---------T 624 (645)
Q Consensus 557 A~WN~eerrl~WkLPdIs~~gg~--G~LrAr~~~~sgpad~ps~P~~~~aVQFsse-Gs~TLSGVdlEl~---------g 624 (645)
|+||++++|++|+||||+..+.. |+|+|||..+.++ ++|.. ++|||.++ |. ||||++|+++ |
T Consensus 164 g~~~~e~~ri~Wrl~el~~~~~~~~~kL~ARf~~~~~~----~~p~~-v~vkF~~~~~~-~~sg~~i~~~~~~~~~dp~~ 237 (257)
T PF10291_consen 164 GTWNKEKNRITWRLPELSLTSEGEGGKLIARFMTSGGP----SRPGG-VEVKFEIEGGS-TLSGLGISLVYQDDEEDPPG 237 (257)
T ss_dssp --B-SSS-EEEEE-SSEEEETT---EEEEEEEEESS--------SS--EEEEEEE---S--SS----EEEEEESSS-TT-
T ss_pred ccccCCCcEEEEECCcccccCCCCCceEEEEEECCCCC----CCCce-EEEEEEEcCCC-cccCcEEEEeecccccCCCC
Confidence 99999999999999999877655 8999999999995 58888 89999999 66 9999999999 9
Q ss_pred CCccceeeccceeccceeecC
Q 044308 625 EGKTDFYEVGHKYESGVYICN 645 (645)
Q Consensus 625 ~Gyr~fslVkkRFaTG~Yl~~ 645 (645)
.+|++ +++||||++|+|+|+
T Consensus 238 ~~w~~-~~~~r~~~sGkY~~~ 257 (257)
T PF10291_consen 238 GGWRL-VLVKRKLVSGKYIAD 257 (257)
T ss_dssp ---EE--EEEEEEEEEEEE--
T ss_pred CcceE-EEEEEEEeeeEEecC
Confidence 99988 999999999999995
No 2
>KOG2398 consensus Predicted proline-serine-threonine phosphatase-interacting protein (PSTPIP) [Cell cycle control, cell division, chromosome partitioning]
Probab=99.97 E-value=3.3e-33 Score=306.12 Aligned_cols=599 Identities=23% Similarity=0.177 Sum_probs=512.4
Q ss_pred cCChhhHHHHHHHHHHHHHHHhhccCCCCCCCCCCCCCccccchhhhhhhc---------ccCCCccccccceeEEeeec
Q 044308 23 WFPPTRALAALSAFRQTREVFAATKRLNPNPQHQSPANISADSESALESIA---------SLGDDPLAASSGQLIVGVES 93 (645)
Q Consensus 23 ~~~~~ra~~a~s~f~~~~~~~a~~k~~~~~~~~~~~~~~~~~~~~~~~si~---------~~gddpla~~sG~~vvgv~~ 93 (645)
|+.+.++.+.+..|.+.|...........+-......+++.-. ...+++. .-++..|...-+++|.+|+.
T Consensus 1 ~~~g~~~~~~l~~F~~eRa~iE~~y~k~~~~l~~k~~~~~~~g-s~~~~~~~~r~~~~~ma~~h~~l~~~l~~~i~~~~k 79 (611)
T KOG2398|consen 1 TKTGLRSTKELADFVRERASIEEDYAKRMGKLAAKAKSYTENG-SFAESWLVMRTSTEAMAKSHLELSRELQDLIKDVAK 79 (611)
T ss_pred CCcccchhhhHHHHHHHHHhhhHHHHHHHHHHhhccccCCCCc-chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5677788888888888885442211110000000111111100 1111111 45677788888899999999
Q ss_pred eeEEEEEEeceEEEEEEeecCCCCCCChhHHHHHHhhheeeEEeeccccccChhhhhhhhhHHHHHHHHhHhccchhHHH
Q 044308 94 RYRVVYRLVNSIYVLGITNADHDNSINVFECINIVNQAVSVIVTACRGVDVTPEKLNRKYAEIYMALDIVLRGVSSIRLA 173 (645)
Q Consensus 94 ~yrv~Yrlvn~iyvl~vt~a~~~~~~nvf~~~~~v~~av~V~v~~~rGvdvtp~kl~rky~evY~ald~vl~g~~~~rla 173 (645)
.|+..|+..+.++..+|..+.+|.+.+.++|...++++++.-+.-|.+.+.+.++..||+...|+++++....+...++.
T Consensus 80 ~~~~~~k~~k~~~~~~v~~~~~~q~~~~~~~~~~~~~~~~~~~~~~~e~e~~~~~~k~~~~~~k~~~~i~~~~~~y~~~~ 159 (611)
T KOG2398|consen 80 YYAEQLKTRKKSKEEGVEKLKQDQSKKKAKDTYEVLCAKSNYLHRCQEKESLKEKEKRKKELAKAELKIKEAREEYRSLV 159 (611)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhhhhcccccchhhHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhccCccchhhhccccchhhhhcCCCCccchhhcchhhhhhhccccccccccchhhhccCcchhhhccccccccccc
Q 044308 174 AMLGSMHGDGIAKMVHSALDTEAKIRGADQWNSLEIHSIEHQAAVDSFSHATFEVPAETLAAGDEVAATLVVQTAAEQDK 253 (645)
Q Consensus 174 a~l~s~h~d~~akm~~sA~d~e~k~rGa~~w~~~~~~~~e~~a~v~~~s~~~Fe~p~etl~Agde~~a~~~P~~~~~~~~ 253 (645)
++|..+|.|-+.+|.+++-..+...++..+|.+.+.+...++...-.+..-.+.-....--.++.+..-|..- +.+..
T Consensus 160 ~~~~~vr~~w~~~~~~~c~~fQ~~Ee~rl~~lk~~l~~~~~~is~~~~~~~q~~E~~k~~le~~sv~~~i~~f-v~~k~- 237 (611)
T KOG2398|consen 160 AKLEKVRKDWEQEMTDLCLKFQEIEESRLSFLKEELWLFANQISESCVKIDQVMEEFKLTLESCSVDEDITKF-VEAKG- 237 (611)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccchhHHHHHHHHhhccCCHHHHHHHH-hhccC-
Confidence 9999999999999999999999999999999999999999999999999888887777777888888777665 33222
Q ss_pred ccCCCCCCCCcCCccchhhcccCCCcccCCcccCCCcc-cccccccccccccCCCCCccCCCcccccccccccccccccc
Q 044308 254 EQEKSEESPTEKDPFAASEAINKEPELVGGFKKNKDSS-NDLTVALAGIEVTTLPPAEATQSTHINVEGFEGEYGGIEFS 332 (645)
Q Consensus 254 ~~~~~~~~~~~~dPfAAs~a~~k~~~L~g~fkk~kd~s-~d~~~~lagl~v~tlpp~~a~~s~~~~veGfeG~yggi~f~ 332 (645)
..+..+.+...++|.+++.+++..++..+|.+.+..+ .++...|+.++++|+...+++.++++++++++|.|+++++.
T Consensus 238 -TGte~P~~i~~e~~~~~~~~~~~~~~~~~~~~~~~~si~~ls~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~v~~~ 316 (611)
T KOG2398|consen 238 -TGTEKPEPIEFENYYSSETIASLVEITSAPSQPKSDSIDGLSLSLAPPEVTTLDKAEHFSSTGPNTPPVDGEITTVESV 316 (611)
T ss_pred -CCCCCCCCCCccccccccccchhhhhhccCCCCccccccchhhccCCcccCchhhhhccCCCCCCCCCcccccCccccc
Confidence 2355666788999999999999999999888888887 99999999999999999999999999999999999999999
Q ss_pred cccchhhhhccCCCCCCCCCCCCccccCCcccccccccccccccccCCCCCCCCCCCCCCCCCccccccccccCCceEEE
Q 044308 333 NDQATMEETFEGFSDAWGGGLDASEFVGPKKIAKKEGLSGLELLQTGPDAPAPSSKDGAGTPLDNLVKRTEMKGPEMYIV 412 (645)
Q Consensus 333 ~~~a~~~~afeg~~d~wgggldasef~~~~~~~k~~gl~g~ell~~g~~~aa~~a~~~~~~~l~~lv~~~e~~~p~~afT 412 (645)
++|..-++.+.-|..+|.||++.+.|.+++.+++..+..+.+++.+.+.... ....+ +++++..+.+++..+.
T Consensus 317 ~~~~~~a~p~~~~~s~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~---~~~~~----~~~~~~~~~~~e~~~s 389 (611)
T KOG2398|consen 317 NSQNVPAEPEQSFSSSWDGGLEPSGPTGPKTIPKKPRNPVSELNLTEAPKTV---TPGDG----TFIKEKQSSTPESPIS 389 (611)
T ss_pred ccccCcCCccccccCCCccccCCCcccCCCCCCCCCCCCCCCcccccccccc---cCCcc----ceeccCCCCCccCccc
Confidence 9999999999999999999999999999999999999999999987554443 22323 7788889999999999
Q ss_pred EEEEEEEecceeEEEeeeeEEEEEecCCCCCCCCCceeEEEEEeccchhhhhcccccccccCCCcceEEecCCCCCCcce
Q 044308 413 EQVNAEFRESLLARVGLMGAVYLRTMPKKTSGDDKDTEFSFRVEGTSAVKRFAVQSSKVSSLGDGMFHVRTAPSDEPIPI 492 (645)
Q Consensus 413 E~inA~FkGs~LvRVG~~GiVrvfT~~P~pa~~~k~~vlSFRL~~tS~Vk~F~pns~l~~S~~tgdF~vr~~aSyynVpI 492 (645)
+.+...+......+.+.+ ..|+.|+...+-+.+++|++-. -..+.+.+...+..|...++++.|+.+|..+..+
T Consensus 390 ~~~~~~~~~~~~~~~~~~----t~tss~~s~~s~~~~~~S~~ss--~~~~s~~~~~~~~~s~~~~~~~~~~~~s~~~~~~ 463 (611)
T KOG2398|consen 390 FEIGTGKPPRPLTAPSVM----TVTSSPNSSDSSKPGAFSGTSS--RKRKSVDELRSRISSPSPGSPGSRTRPSPTLPGI 463 (611)
T ss_pred ccccccCCCCCCCccccc----cccCCCCCCCCCCCCCcCcccc--cccCCchhhccCCCCCCCCCCCCCCCCCcccccc
Confidence 999998888777666655 7788888888889999999877 3468889999999999999999999999999999
Q ss_pred EEeeeCCCCCCCCcEEEEEEeecCceEEEEEEEEeCCCCCCCccceEEEeecCCCCCccccccccccccccceeeEEccC
Q 044308 493 LRYSLLPRLTPLPLRVRLIKRHSGTLLSVMVQYVSNPDLPMPLNDVTFSLKLPVDPTLLKVSPKAVLNRSDRELKWIVPE 572 (645)
Q Consensus 493 LKYql~pg~~p~PL~lr~~wk~~~tlt~V~VdY~yNP~lp~PLtnVq~iL~VPvd~tlLqs~P~A~WN~eerrl~WkLPd 572 (645)
. |-+.|...+.+++.+.-|...+ ++++.+|..+|++..||++.+...+.+..+++...++...+|.......|-.+.
T Consensus 464 ~-~~~~p~~s~~~~~s~~p~~~~~--~~~~~~s~~~p~s~~p~~~~~~~~~~~~~p~~~~~~~~~~l~~~~~~~~~g~s~ 540 (611)
T KOG2398|consen 464 R-APLRPSSSPSPSSSRPPKAISG--LRLDPISVAMPDSSNPLTDADSPSVDDESPSLTKTSRGNILNLTGVGSSRGPSP 540 (611)
T ss_pred c-CCCCccCCccccccCCCccccc--cccccccccCCCCCCchhhhcccccccccccccccCccccccccccccCCCCCc
Confidence 9 9999999999999999998888 777889999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCc--eEEEEeecCCCCCCCCCccceEEEEEEeecCCccccceeeeecCCCccceeeccceeccceeecC
Q 044308 573 IPVKGAPG--KLRVRMPVDSSEEDGGEEIDVVCHVKFASQGMLSLSGVCLRPATEGKTDFYEVGHKYESGVYICN 645 (645)
Q Consensus 573 Is~~gg~G--~LrAr~~~~sgpad~ps~P~~~~aVQFsseGs~TLSGVdlEl~g~Gyr~fslVkkRFaTG~Yl~~ 645 (645)
|...+.+| .+.|..+..+- .- ..+...|.|.|+.++.+++.+. ++..-.|..++..+-+|...++|||+
T Consensus 541 ~~~~~s~~~~i~~a~~~~~~~--~~-~~~~~s~~~~~~~~~~~s~~~~-i~~~~~~n~~~~~~~fr~~~~~~~~~ 611 (611)
T KOG2398|consen 541 ITLGGSDGLPIAAAFAEIVHA--YF-EGPDESCIVKDTGEMMLSFPAG-ITGLVAGNPDPARLDFRLLNVRNIEN 611 (611)
T ss_pred ccCCCCCcchhhhhhhhcchh--hh-cCCCcceeeeeeEEEEEeeccc-hhhhhcCCCCccccccccccceeccC
Confidence 98777888 88888877754 22 2233339999999999999999 99999999999999999999999995
No 3
>PF00928 Adap_comp_sub: Adaptor complexes medium subunit family; InterPro: IPR008968 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. This entry represents the C-terminal domain of the mu subunit from various clathrin adaptors (AP1, AP2 and AP3) []. The C-teminal domain has an immunoglobulin-like beta-sandwich fold consisting of 9 strands in 2 sheets with a Greek key topology, similar to that found in cytochrome f and certain transcription factors []. The mu subunit regulates the coupling of clathrin lattices with particular membrane proteins by self-phosphorylation via a mechanism that is still unclear []. The mu subunit possesses a highly conserved N-terminal domain of around 230 amino acids, which may be the region of interaction with other AP proteins; a linker region of between 10 and 42 amino acids; and a less well-conserved C-terminal domain of around 190 amino acids, which may be the site of specific interaction with the protein being transported in the vesicle []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 1H6E_A 3L81_A 1W63_V 4EMZ_A 4EN2_A 2VGL_M 3ML6_F 2PR9_A 2JKT_M 1I31_A ....
Probab=99.49 E-value=1.7e-12 Score=126.32 Aligned_cols=226 Identities=19% Similarity=0.277 Sum_probs=156.8
Q ss_pred ceEEEEEEEEEEe-cceeEEEeeeeEEEEEecCCCCCCCCCceeEEEEEecc-------chhhhhcccccccccCCCcce
Q 044308 408 EMYIVEQVNAEFR-ESLLARVGLMGAVYLRTMPKKTSGDDKDTEFSFRVEGT-------SAVKRFAVQSSKVSSLGDGMF 479 (645)
Q Consensus 408 ~~afTE~inA~Fk-Gs~LvRVG~~GiVrvfT~~P~pa~~~k~~vlSFRL~~t-------S~Vk~F~pns~l~~S~~tgdF 479 (645)
-+-++|.|++.+. .+.+.+.-+.|.|.+..-....+ .++++|.+. ..++++.--.....+.-..+=
T Consensus 16 ~vdv~E~i~~~~~~~G~~~~~~v~G~v~~~~~l~g~p------~i~l~l~~~~~~~~~~~~l~~~~fH~cV~~~~~~~~~ 89 (262)
T PF00928_consen 16 FVDVVEKISAVLDRDGNILSSEVKGSVQCKSFLSGMP------EIKLTLNNPLVVSKNGIKLDDVSFHPCVDLSKFESDR 89 (262)
T ss_dssp EEEEEEEEEEEEETTSEEEEEEEEEEEEEEEE-SST-------EEEEEESSSCCCTSSSBEESEEEEETTEECCCCCSHT
T ss_pred EEEEEEEEEEEEccCCcEEEEEEEEEEEEEEeCCCCC------eEEEEecCccccccCceeeeceeeccccCcccccccc
Confidence 4568999999987 57788888999999998766666 788888876 445443322222111111122
Q ss_pred EEecCCCCCCcceEEeeeCCCCCCCCcEEEEEEee-cCceEEEEEEEEeCCCCCCCccceEEEeecCCCCC--cccc-cc
Q 044308 480 HVRTAPSDEPIPILRYSLLPRLTPLPLRVRLIKRH-SGTLLSVMVQYVSNPDLPMPLNDVTFSLKLPVDPT--LLKV-SP 555 (645)
Q Consensus 480 ~vr~~aSyynVpILKYql~pg~~p~PL~lr~~wk~-~~tlt~V~VdY~yNP~lp~PLtnVq~iL~VPvd~t--lLqs-~P 555 (645)
-+...|+.-.+++|+|++... .++|+.+...|.. +...++++|+|..|......+.||.|.+|+|.... .+++ .-
T Consensus 90 ~i~f~PPdg~f~Ll~Yr~~~~-~~~P~~i~~~~~~~~~~~~~v~i~~~~~~~~~~~~~~v~I~iplP~~~~~~~~~~~~G 168 (262)
T PF00928_consen 90 VISFIPPDGEFTLLRYRVSSN-SPLPFKITCWVSEKSSGRFEVTIELESNFPNKISLENVVIRIPLPPGTSSPSIESSDG 168 (262)
T ss_dssp EEEE---SEEEEEEEEEEESS-S--SEEEEEEEEEETTTEEEEEEEEEE-S-TTSEEEEEEEEEE--TTEEEEEEEESSS
T ss_pred ceecCCCCceEEEEEEEccCC-CCCCcEEEEEeccCCCceEEEEEEecccCCCCceeceEEEEeecCCccccceeeecCc
Confidence 344467777999999999766 8999999887776 78888999999998766789999999999996654 4443 44
Q ss_pred ccccccccceeeEEccCCCCCCCCceEEEEeecCCCCCCCCC--ccceEEEEEEeecCCccccceeeeecC-----CCcc
Q 044308 556 KAVLNRSDRELKWIVPEIPVKGAPGKLRVRMPVDSSEEDGGE--EIDVVCHVKFASQGMLSLSGVCLRPAT-----EGKT 628 (645)
Q Consensus 556 ~A~WN~eerrl~WkLPdIs~~gg~G~LrAr~~~~sgpad~ps--~P~~~~aVQFsseGs~TLSGVdlEl~g-----~Gyr 628 (645)
.+.|+.+++.+.|+|+.|+. +..-.|++++.+.... +.+. .-.+ +.|.|..+|. ++||+.++-.. ++|.
T Consensus 169 ~~~~~~~~~~l~W~I~~~~~-~~~~~l~~~l~~~~~~-~~~~~~~~~p-i~v~F~~~~~-~~Sgl~V~~l~v~~~~~~~~ 244 (262)
T PF00928_consen 169 SAEYDEEENALVWKIKKLPG-GSESTLSGTLEFSSPS-SVPSDWSFFP-ISVEFTIPGY-TLSGLKVRSLDVVNEDENYK 244 (262)
T ss_dssp EEEEETGCTEEEEEEEEEET-SEEEEEEEEEEEEEEC-CSS-S------EEEEEEESTS-ETTT-EEEEEEEE-SSCGGG
T ss_pred eEEEEccCCEEEEEECCccC-cccccEEEEEEecCCC-ccccccccee-EEEEEEeCCc-ccCCCEEEEEEeEecCCCCC
Confidence 58899999999999999963 3445677777665542 1122 2223 7999999998 99999876643 7999
Q ss_pred ceeeccceeccceeec
Q 044308 629 DFYEVGHKYESGVYIC 644 (645)
Q Consensus 629 ~fslVkkRFaTG~Yl~ 644 (645)
-+.-||.--.+|.|-+
T Consensus 245 ~~k~vky~t~s~~Y~i 260 (262)
T PF00928_consen 245 PYKWVKYVTKSGSYEI 260 (262)
T ss_dssp SEEEEEEEEEEEEEEE
T ss_pred CcccEEEEEEcCcEEE
Confidence 9999999999999965
No 4
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.88 E-value=3.8e-06 Score=91.18 Aligned_cols=167 Identities=19% Similarity=0.326 Sum_probs=118.2
Q ss_pred cccccccccCCCcceEEec----CCCCCCcceEEeeeCC-CCCCCCcEEEEEEeecCceEEEEEEEEeCCCCCCCccceE
Q 044308 465 AVQSSKVSSLGDGMFHVRT----APSDEPIPILRYSLLP-RLTPLPLRVRLIKRHSGTLLSVMVQYVSNPDLPMPLNDVT 539 (645)
Q Consensus 465 ~pns~l~~S~~tgdF~vr~----~aSyynVpILKYql~p-g~~p~PL~lr~~wk~~~tlt~V~VdY~yNP~lp~PLtnVq 539 (645)
-||.++....++.-..+|+ =|-..+|.+||++... ....+||-+.+.=.-++.-++|+|+|-. .+-.-|+||-
T Consensus 333 HPNlDK~~f~s~s~iglk~~~K~FPvn~~VGvLkWR~~~~des~iPlTincWPSes~~g~dV~iEYe~--~~~~eL~dV~ 410 (512)
T KOG2635|consen 333 HPNLDKKVFLSSSLIGLKRPEKPFPVNSDVGVLKWRMVDEDESEIPLTINCWPSESGNGYDVNIEYEA--VLECELNDVI 410 (512)
T ss_pred CCCcchhhhccccccccccCCCCCCcCCcceEEEEeecccccccCceEEEeccccCCCCeEEEEEEee--hhcccccceE
Confidence 3555544333333334443 2456899999999985 7899999998877777777999999976 6678999999
Q ss_pred EEeecCCCCC-ccccccccccc--cccceeeEEccCCCCCCCCceEEEEeecCCCCCCCCCccceEEEEEEeecCCcccc
Q 044308 540 FSLKLPVDPT-LLKVSPKAVLN--RSDRELKWIVPEIPVKGAPGKLRVRMPVDSSEEDGGEEIDVVCHVKFASQGMLSLS 616 (645)
Q Consensus 540 ~iL~VPvd~t-lLqs~P~A~WN--~eerrl~WkLPdIs~~gg~G~LrAr~~~~sgpad~ps~P~~~~aVQFsseGs~TLS 616 (645)
|.+|||.+.. .+. .=-+.|+ ..++-+-|+|+.| .++-+|+|-=+.++... ..-=| +.|+|++.- +.+
T Consensus 411 i~iPlP~~iapsv~-~~Dge~~~~~~~~~leW~I~~I-a~N~SGslEFs~~~~~~-----~~fFP-l~VsF~s~~--~ft 480 (512)
T KOG2635|consen 411 ITIPLPANIAPSVG-ECDGEYRYDERKNVLEWSIGVI-AKNFSGSLEFSCPASDP-----DGFFP-LSVSFTSDT--VFT 480 (512)
T ss_pred EEeecccccCCccc-eecceEEeccccceeEEEeeee-ccCCCCcEEEeecCCCC-----Cceee-EEEEEEecc--ccc
Confidence 9999996653 111 1124554 3455689999999 68999999877665533 33334 789999984 788
Q ss_pred ceeeee---cCCCccceeeccceeccceee
Q 044308 617 GVCLRP---ATEGKTDFYEVGHKYESGVYI 643 (645)
Q Consensus 617 GVdlEl---~g~Gyr~fslVkkRFaTG~Yl 643 (645)
|+-++- ..++-..=+.++..|..-+|.
T Consensus 481 gl~vqkVv~~~~~~~~~y~~~t~f~~dky~ 510 (512)
T KOG2635|consen 481 GLFVQKVVRNDGHAPVRYSVETTFEVDKYE 510 (512)
T ss_pred ceEEEEEEEcCCCCCceeEEEEEEEeeeeE
Confidence 987653 343344447788888888885
No 5
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.46 E-value=6.5e-06 Score=89.02 Aligned_cols=206 Identities=21% Similarity=0.319 Sum_probs=149.9
Q ss_pred eEEEEEEE-EEEecceeEEEeeeeEEEEEecCCCCCCCCCceeEEEEEeccchhhhhccccccc-ccCCC----------
Q 044308 409 MYIVEQVN-AEFRESLLARVGLMGAVYLRTMPKKTSGDDKDTEFSFRVEGTSAVKRFAVQSSKV-SSLGD---------- 476 (645)
Q Consensus 409 ~afTE~in-A~FkGs~LvRVG~~GiVrvfT~~P~pa~~~k~~vlSFRL~~tS~Vk~F~pns~l~-~S~~t---------- 476 (645)
+-++|.|| .+++++.+.+.=+.|.|+.+.-..--+ +++|-|....-.+.-.+.+.-. ...++
T Consensus 171 lDViE~Vs~l~~~~G~vl~s~i~G~I~~k~~LsGmP------elrl~ln~~~~~~~~~~~~~s~~v~ledi~fh~~v~l~ 244 (424)
T KOG0937|consen 171 LDVIESVSLLYDSNGIVLLSEIVGTIKLKCYLSGMP------ELRLGLNDKVLFDKQGPRSKSKGVELEDIKFHECVRLS 244 (424)
T ss_pred EEhhhhhhHhhhcCCcEEEeeeeeEEEEEEEcCCCc------eeeeecCcccccccccccccCcceEeeecccceeechh
Confidence 45679999 899999999999999999997776666 7888777665554332211111 01122
Q ss_pred ---cceEEecCCCCCCcceEEeeeCCCCCCCCcEEEEEEeecCceEEEEEEEEeCCCCCCCccceEEEeecCCCCCcc--
Q 044308 477 ---GMFHVRTAPSDEPIPILRYSLLPRLTPLPLRVRLIKRHSGTLLSVMVQYVSNPDLPMPLNDVTFSLKLPVDPTLL-- 551 (645)
Q Consensus 477 ---gdF~vr~~aSyynVpILKYql~pg~~p~PL~lr~~wk~~~tlt~V~VdY~yNP~lp~PLtnVq~iL~VPvd~tlL-- 551 (645)
.|..+...|+.-+.++|+||++-...|+=.-=++.++|+.....+++.-+.+=....--+||+|.+|||-+...+
T Consensus 245 ~fd~dr~i~FiPPdGeF~Lm~Y~ls~~vkPli~~~~~~~~~~~~ri~i~~K~~~~fk~~~~a~~v~I~iP~P~~a~~~~f 324 (424)
T KOG0937|consen 245 RFDNDRTISFIPPDGEFELMRYRLSTHVKPLIWFYQLIEEHSRSRIEVMVKLREQFKSRSSANNVEICIPVPDDASSPSF 324 (424)
T ss_pred hccCCceEEecCCCCceEEEEEEecCCCCCeEEeeeeeeeccceeEEEEEechhhcCCccccceEEEEeeCCCccccceE
Confidence 223444579999999999999976665555556777888888888887766666777788999999999888755
Q ss_pred c-cccccccccccceeeEEccCCCCCCCCc-eEEEEeecCCCCCC--CCCccceEEEEEEeecCCccccceeeeecC
Q 044308 552 K-VSPKAVLNRSDRELKWIVPEIPVKGAPG-KLRVRMPVDSSEED--GGEEIDVVCHVKFASQGMLSLSGVCLRPAT 624 (645)
Q Consensus 552 q-s~P~A~WN~eerrl~WkLPdIs~~gg~G-~LrAr~~~~sgpad--~ps~P~~~~aVQFsseGs~TLSGVdlEl~g 624 (645)
+ +.+.+.+++|++-|+|.|.... |+.- .+|++|.+-+.+.. ....-.+ +.|.|-=-.- |.||+.++-..
T Consensus 325 k~s~G~~~~~~e~~~l~W~I~~~~--gg~e~~~r~~~~lp~~~~e~~~~~~~~p-i~v~FeIp~~-T~SgiqVrylk 397 (424)
T KOG0937|consen 325 KTSLGSAKYDPEKSALRWTIKKFV--GGKEYSLRARMDLPSEEHEEQCTEGLGP-IKVKFEIPYF-TVSGIQVRYLK 397 (424)
T ss_pred eccCCceeeecccceEEEEecccc--CCceEEEEEeecCCccccCCCCcccCCc-eEEEEEeccc-ccCCeEEEEEE
Confidence 3 4566999999999999999886 3333 88999866555311 1233344 6899999988 99999887654
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=97.10 E-value=0.0032 Score=57.48 Aligned_cols=71 Identities=18% Similarity=0.421 Sum_probs=61.7
Q ss_pred eceeEEEEEEeceEEEEEEeecCCCCCCChhHHHHHHhhheeeEEeeccccccChhhhhhhhhHHHHHHHHhHhccc
Q 044308 92 ESRYRVVYRLVNSIYVLGITNADHDNSINVFECINIVNQAVSVIVTACRGVDVTPEKLNRKYAEIYMALDIVLRGVS 168 (645)
Q Consensus 92 ~~~yrv~Yrlvn~iyvl~vt~a~~~~~~nvf~~~~~v~~av~V~v~~~rGvdvtp~kl~rky~evY~ald~vl~g~~ 168 (645)
...|+++|+-.+.+|+..++..+ .|....+++++.-+.++=..++ +|+...|..+|..||++||-++-++-
T Consensus 52 ~~~~~~vy~~~~dl~~~~v~~~~----eNel~~~e~l~~~v~~l~~~~~--~v~e~~i~~N~~~v~~~LDEiid~G~ 122 (141)
T PF01217_consen 52 HDNYRIVYKRYSDLYFVVVGDEN----ENELLLLEFLHRLVEVLDDYFG--NVSEKDILENFDLVYLILDEIIDGGI 122 (141)
T ss_dssp ETTEEEEEEEETTEEEEEEESST----SBHHHHHHHHHHHHHHHHHHHS--S-SHHHHHHTHHHHHHHHHHHEETTE
T ss_pred cccceeeeEeeccEEEEEEeecc----cchHHHHHHHHHhhhhhhhhhc--cccHHHHHHCHHHHHHHHHHHHhCCE
Confidence 45699999999999999999433 6999999999999999888888 88999999999999999998887753
No 7
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=96.07 E-value=0.63 Score=50.75 Aligned_cols=226 Identities=22% Similarity=0.340 Sum_probs=133.1
Q ss_pred ccccccCCceEEEEEEEEEEe-cceeEEEeeeeEEEEEecCCCCCCCCCceeEEEEEeccchhhh-------------hc
Q 044308 400 KRTEMKGPEMYIVEQVNAEFR-ESLLARVGLMGAVYLRTMPKKTSGDDKDTEFSFRVEGTSAVKR-------------FA 465 (645)
Q Consensus 400 ~~~e~~~p~~afTE~inA~Fk-Gs~LvRVG~~GiVrvfT~~P~pa~~~k~~vlSFRL~~tS~Vk~-------------F~ 465 (645)
+|.|+ =+.+.|.+|---- .+.+.|.-+.|.|..+|..--.| +..|-|...=.+|. |-
T Consensus 176 kknev---fldvvErvNlLmS~~GnVLrs~VsG~V~mk~~LSGmP------eckfGlNDkl~~e~kq~esks~~~n~~~~ 246 (446)
T KOG0938|consen 176 KKNEV---FLDVVERVNLLMSSDGNVLRSDVSGTVDMKTHLSGMP------ECKFGLNDKLGMESKQSESKSDFGNKNFP 246 (446)
T ss_pred cccee---EeEehheeeeEEcCCCCEEEeecccEEEEEEeccCCc------ccccccCcccceeeccccccccccccCCC
Confidence 66655 4678899986553 35688888999999998877666 77777776555442 11
Q ss_pred cccccccc-CCCcceEE-------------ecCCCCCCcceEEeeeCCCCCCCCcEEEEEEeecC-ceEEEEEEEEeCCC
Q 044308 466 VQSSKVSS-LGDGMFHV-------------RTAPSDEPIPILRYSLLPRLTPLPLRVRLIKRHSG-TLLSVMVQYVSNPD 530 (645)
Q Consensus 466 pns~l~~S-~~tgdF~v-------------r~~aSyynVpILKYql~pg~~p~PL~lr~~wk~~~-tlt~V~VdY~yNP~ 530 (645)
+.+...+- .++--||= ...|+.--+-+|||++.-.+ -+|+|+.-..++.+ +.+.++|-.+++
T Consensus 247 sks~~g~v~leDc~FHqCV~L~kFn~eh~IsFvPPDGe~ELMkYr~~enI-nlPFrV~PiV~el~r~kie~ri~iks~-- 323 (446)
T KOG0938|consen 247 SKSGKGSVLLEDCTFHQCVRLDKFNSEHIISFVPPDGEFELMKYRVTENI-NLPFRVTPIVTELGRTKIEYRITIKSL-- 323 (446)
T ss_pred cccCCceEEeeccchheeeccccccccceEEEeCCCCceEeEeeeeccCc-ccceEeeeheecccceeEEEEEEEecc--
Confidence 11111000 02223332 12578888999999998655 47888887776654 445555555543
Q ss_pred CCCCccceEEEeecCCCCC----cccc-ccccccccccceeeEEccCCCCCCC-CceEEEEeecCCCCCCCC--CccceE
Q 044308 531 LPMPLNDVTFSLKLPVDPT----LLKV-SPKAVLNRSDRELKWIVPEIPVKGA-PGKLRVRMPVDSSEEDGG--EEIDVV 602 (645)
Q Consensus 531 lp~PLtnVq~iL~VPvd~t----lLqs-~P~A~WN~eerrl~WkLPdIs~~gg-~G~LrAr~~~~sgpad~p--s~P~~~ 602 (645)
-|+-|..-.+.+++|+.+. +.++ .=+|-++++++-+.||++... |- --.|.|..+++.--.+.- -+|..+
T Consensus 324 f~~kl~a~~v~~rIPvP~ntv~~n~~v~~Gkaky~psen~ivWki~kf~--G~tE~tlsAevels~Tt~nkq~WtrPPIs 401 (446)
T KOG0938|consen 324 FPPKLLAKDVVVRIPVPPNTVKCNISVSNGKAKYVPSENAIVWKINKFN--GLTESTLSAEVELSDTTQNKQQWTRPPIS 401 (446)
T ss_pred CCchhhhcceEEEecCCCccccceeEEecCccccCcccceEEEEecccC--CcccceeEEEEEeccCccccccccCCCce
Confidence 3344444444444455444 4444 335999999999999999884 32 348999998886521111 125443
Q ss_pred EEEEEeecCCccccceeeeec-----CCCccceeeccceecccee
Q 044308 603 CHVKFASQGMLSLSGVCLRPA-----TEGKTDFYEVGHKYESGVY 642 (645)
Q Consensus 603 ~aVQFsseGs~TLSGVdlEl~-----g~Gyr~fslVkkRFaTG~Y 642 (645)
+-.+-. ++|=||+.++-. -++|+--.-|+---.+|.|
T Consensus 402 leFeV~---MFt~SGL~VrylkV~e~~Sk~~~vkWVrYitkaGsy 443 (446)
T KOG0938|consen 402 LEFEVP---MFTNSGLVVRYLKVSEKDSKHRAVKWVRYITKAGSY 443 (446)
T ss_pred eEEeee---eecCCceEEEEEEEecccCCCceEEEEEEeccccee
Confidence 333322 235577766532 2355443334333344555
No 8
>KOG2398 consensus Predicted proline-serine-threonine phosphatase-interacting protein (PSTPIP) [Cell cycle control, cell division, chromosome partitioning]
Probab=93.05 E-value=0.026 Score=64.28 Aligned_cols=51 Identities=18% Similarity=0.199 Sum_probs=43.6
Q ss_pred CceEEEEEEEEEEecce---eEEE-e------eeeEEEEEecCCCCCCCCCceeEEEEEeccchhhh
Q 044308 407 PEMYIVEQVNAEFRESL---LARV-G------LMGAVYLRTMPKKTSGDDKDTEFSFRVEGTSAVKR 463 (645)
Q Consensus 407 p~~afTE~inA~FkGs~---LvRV-G------~~GiVrvfT~~P~pa~~~k~~vlSFRL~~tS~Vk~ 463 (645)
=.+||+|++|+||+|.+ ++|+ | +.||.+++..+|.+. .+.||+.++..|++
T Consensus 551 i~~a~~~~~~~~~~~~~~s~~~~~~~~~~~s~~~~i~~~~~~n~~~~------~~~fr~~~~~~~~~ 611 (611)
T KOG2398|consen 551 IAAAFAEIVHAYFEGPDESCIVKDTGEMMLSFPAGITGLVAGNPDPA------RLDFRLLNVRNIEN 611 (611)
T ss_pred hhhhhhhcchhhhcCCCcceeeeeeEEEEEeeccchhhhhcCCCCcc------ccccccccceeccC
Confidence 36899999999999977 5554 4 469999999999999 99999999998875
No 9
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.07 E-value=9.6 Score=42.22 Aligned_cols=218 Identities=15% Similarity=0.164 Sum_probs=122.7
Q ss_pred EEEEEEEEEEe-cceeEEEeeeeEEEEEecCCCCCCCCCceeEEEEEeccchhhhhcccccccccCCCcceE--EecCCC
Q 044308 410 YIVEQVNAEFR-ESLLARVGLMGAVYLRTMPKKTSGDDKDTEFSFRVEGTSAVKRFAVQSSKVSSLGDGMFH--VRTAPS 486 (645)
Q Consensus 410 afTE~inA~Fk-Gs~LvRVG~~GiVrvfT~~P~pa~~~k~~vlSFRL~~tS~Vk~F~pns~l~~S~~tgdF~--vr~~aS 486 (645)
-+.|+++|-|. .++++..-+.|+|.+....---| ...+||+ |..-+...---.+... ....+| +...|+
T Consensus 183 dvlEeidai~~k~gslv~~eI~g~vd~~~qLsgmP----dltlsl~--np~~L~dvsfHpcVr~--krwe~~~~lsFIPP 254 (418)
T KOG2740|consen 183 DVLEEIDAIVDKKGSLVFGEIQGIVDVCSQLSGMP----DLTLSLN--NPRLLGDVSFHPCVRY--KRWESHSVLSFIPP 254 (418)
T ss_pred hhhheeheEecCCCCEEEEEEEEEEEEEEeecCCC----ceEEEcc--CccccCCcccccceee--cccccccceEEcCC
Confidence 35788888874 46688888999998884322211 2245554 2222211100000000 112222 123688
Q ss_pred CCCcceEEeeeCC-CCCCCCcEEEEEEeecCceEEEEEEEEeCCCC--CCC--ccceEEEeecCCCCCccccccc---cc
Q 044308 487 DEPIPILRYSLLP-RLTPLPLRVRLIKRHSGTLLSVMVQYVSNPDL--PMP--LNDVTFSLKLPVDPTLLKVSPK---AV 558 (645)
Q Consensus 487 yynVpILKYql~p-g~~p~PL~lr~~wk~~~tlt~V~VdY~yNP~l--p~P--LtnVq~iL~VPvd~tlLqs~P~---A~ 558 (645)
.-++-+|.||+.. ..-..|.-+.-.-.-.+.. +++++.---|.. -.- +-+|++-+ |-..-++-..|. -+
T Consensus 255 DGkFrLlsy~v~~~~~v~~pvyv~~~i~l~~~~-~~ri~~tvg~~~~~gK~ie~itVt~~~--pn~i~~~~k~~~~g~~~ 331 (418)
T KOG2740|consen 255 DGKFRLLSYRVDAQNQVAIPVYVKNSISLDSNH-QGRISLTVGPKKKMGKTIELITVTVQD--PNEIAYASKILTHGTFT 331 (418)
T ss_pred CCcEEEEEEEEehhhccccceEEeeeeccCCCc-eEEEEEeccccccccceeEeEEEEecC--ccceeeeecccccceeE
Confidence 9999999999974 5566665554433322222 333333333321 111 22444444 644443333332 33
Q ss_pred cccccceeeEEccCCCCCCCCceEEEEeecCCCCCCCCCccceEEEEEEeecCCccccceeee---ecCCCccceeeccc
Q 044308 559 LNRSDRELKWIVPEIPVKGAPGKLRVRMPVDSSEEDGGEEIDVVCHVKFASQGMLSLSGVCLR---PATEGKTDFYEVGH 635 (645)
Q Consensus 559 WN~eerrl~WkLPdIs~~gg~G~LrAr~~~~sgpad~ps~P~~~~aVQFsseGs~TLSGVdlE---l~g~Gyr~fslVkk 635 (645)
....-|.+.|-+-.|. +|---.|+--+.+..|. ..+.+-.. +-.||.-+|. +|||+.+| ..|.=|+.|.=||+
T Consensus 332 ~~~~~k~l~W~~~~i~-tg~lp~Lkg~~~~e~~~-sk~~~l~t-~~Lqykiqg~-alsglkVe~Ldm~~~~~k~yKGvKy 407 (418)
T KOG2740|consen 332 NSIIMKQLTWTFGSIA-TGKLPVLKGTINLEPGF-SKKVDLPT-LSLQYKIQGQ-ALSGLKVERLDMYGEPYKPYKGVKY 407 (418)
T ss_pred eecccceeEEEeeccc-CCcccccccccccCCCC-CccccCcc-cceeeeeeee-eccceEEEeeeecCCCCccccceEE
Confidence 3445788999886664 33333566666666553 33344334 6899999999 99999877 56777888888888
Q ss_pred eecccee
Q 044308 636 KYESGVY 642 (645)
Q Consensus 636 RFaTG~Y 642 (645)
.-.+|.+
T Consensus 408 ~t~agnf 414 (418)
T KOG2740|consen 408 KTKAGNF 414 (418)
T ss_pred EEeeeeE
Confidence 8888876
No 10
>KOG2677 consensus Stoned B synaptic vesicle biogenesis protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=75.90 E-value=11 Score=44.46 Aligned_cols=137 Identities=16% Similarity=0.259 Sum_probs=95.1
Q ss_pred CCCCcceEEeeeCCCCCCCCcEEEEEEeecCceEEEEEEEE--------eCCCCCCCccceEEEeecCCCCC-cc-----
Q 044308 486 SDEPIPILRYSLLPRLTPLPLRVRLIKRHSGTLLSVMVQYV--------SNPDLPMPLNDVTFSLKLPVDPT-LL----- 551 (645)
Q Consensus 486 SyynVpILKYql~pg~~p~PL~lr~~wk~~~tlt~V~VdY~--------yNP~lp~PLtnVq~iL~VPvd~t-lL----- 551 (645)
.---+-||+|+..+--.-+|+-|+...+..|..+.|.+.-. ..|...-|-.||.|-.|||..=. ++
T Consensus 685 DaCrFElMRFrt~~~~~~lpftlks~~~V~Ga~VEvq~~~~mat~~qr~rd~~~~vpCenI~IrfPVPs~WIk~fr~e~~ 764 (922)
T KOG2677|consen 685 DACRFELMRFRTVFAEKTLPFTLKSATSVNGAEVEVQSWLRMATGFQRNRDPLTQVPCENIMIRFPVPSEWIKNFRRESV 764 (922)
T ss_pred ccceeeeeeeeeecCCCcCceeeeeeeeeccceeehHHHHHHHhhhhhccCccccCcccceeEeccCcHHHHHHHHHHhh
Confidence 33445688888876445899999999998888877743221 12335567788889887774322 11
Q ss_pred -------------------cc--ccc--------cccccccceeeEEccCCCCCC----CCceEEEEeecCCCCCCCCCc
Q 044308 552 -------------------KV--SPK--------AVLNRSDRELKWIVPEIPVKG----APGKLRVRMPVDSSEEDGGEE 598 (645)
Q Consensus 552 -------------------qs--~P~--------A~WN~eerrl~WkLPdIs~~g----g~G~LrAr~~~~sgpad~ps~ 598 (645)
+. +|+ |-.--.=+.+.|+|+.+++|. -|--|.-++++.+.- ..|++
T Consensus 765 ~g~kSlkaK~nR~a~~gsl~~~~sepvi~vt~G~AKYEhay~siVWrI~RLPdKnsa~~hpHcl~c~lELgSd~-evPs~ 843 (922)
T KOG2677|consen 765 LGEKSLKAKVNRGASFGSLSVSGSEPVIRVTLGTAKYEHAYNSIVWRINRLPDKNSASGHPHCLFCHLELGSDR-EVPSR 843 (922)
T ss_pred hccchhhhhhcccccccchhhccCCceEEEeecchhhHHhhhhheeecccCCccccccCCCeeEEEEEeccccc-cCchh
Confidence 10 111 222223367999999999884 355799999999984 55677
Q ss_pred cceEEEEEEeecCCccccceeeeecC
Q 044308 599 IDVVCHVKFASQGMLSLSGVCLRPAT 624 (645)
Q Consensus 599 P~~~~aVQFsseGs~TLSGVdlEl~g 624 (645)
=.+.+-|+||+.-+ |-|.-.++.+|
T Consensus 844 f~p~~~V~FsmP~t-~aS~t~VRSis 868 (922)
T KOG2677|consen 844 FAPHVNVEFSMPTT-SASKTSVRSIS 868 (922)
T ss_pred hccccceeeecccc-ccccceeeeee
Confidence 67778999999987 99988888766
No 11
>PF02883 Alpha_adaptinC2: Adaptin C-terminal domain; InterPro: IPR008152 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 []. GGAs (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) are a family of monomeric clathrin adaptor proteins that are conserved from yeasts to humans. GGAs regulate clathrin-mediated the transport of proteins (such as mannose 6-phosphate receptors) from the TGN to endosomes and lysosomes through interactions with TGN-sorting receptors, sometimes in conjunction with AP-1 [, ]. GGAs bind cargo, membranes, clathrin and accessory factors. GGA1, GGA2 and GGA3 all contain a domain homologous to the ear domain of gamma-adaptin. GGAs are composed of a single polypeptide with four domains: 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 VHS domain is responsible for endocytosis and signal transduction, recognising transmembrane cargo through the ACLL sequence in the cytoplasmic domains of sorting receptors []. The GAT domain (also found in Tom1 proteins) interacts with ARF (ADP-ribosylation factor) to regulate membrane trafficking [], and with ubiquitin for receptor sorting []. The hinge region contains a clathrin box for recognition and binding to clathrin, similar to that found in AP adaptins. The GAE domain is similar to the AP gamma-adaptin ear domain, and is responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. This entry represents a beta-sandwich structural motif found in the appendage (ear) domain of alpha-, beta- and gamma-adaptin from AP clathrin adaptor complexes, and the GAE (gamma-adaptin ear) domain of GGA adaptor proteins. These domains have an immunoglobulin-like beta-sandwich fold containing 7 or 8 strands in 2 beta-sheets in a Greek key topology [, ]. Although these domains share a similar fold, there is little sequence identity between the alpha/beta-adaptins and gamma-adaptin/GAE. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 3MNM_B 3ZY7_B 1GYU_A 1GYW_B 2A7B_A 1GYV_A 2E9G_A 1E42_B 2G30_A 2IV9_B ....
Probab=56.08 E-value=1.4e+02 Score=26.30 Aligned_cols=89 Identities=12% Similarity=0.251 Sum_probs=50.4
Q ss_pred cEEEEEE--eecCceEEEEEEEEeCCCCCCCccceEEEeecCCCCCccccccccccccccceeeEEccCCCCCCCCceEE
Q 044308 506 LRVRLIK--RHSGTLLSVMVQYVSNPDLPMPLNDVTFSLKLPVDPTLLKVSPKAVLNRSDRELKWIVPEIPVKGAPGKLR 583 (645)
Q Consensus 506 L~lr~~w--k~~~tlt~V~VdY~yNP~lp~PLtnVq~iL~VPvd~tlLqs~P~A~WN~eerrl~WkLPdIs~~gg~G~Lr 583 (645)
|++.+.. .+.+..+++.+.|.-+ .+.+|+|++|.+-|| ..-.|+.+|... ..|+. .+.+.
T Consensus 11 l~I~~~~~~~~~~~~~~i~~~f~N~--s~~~it~f~~q~avp-k~~~l~l~~~s~------------~~i~p---~~~i~ 72 (115)
T PF02883_consen 11 LQIGFKSEKSPNPNQGRIKLTFGNK--SSQPITNFSFQAAVP-KSFKLQLQPPSS------------STIPP---GQQIT 72 (115)
T ss_dssp EEEEEEEEECCETTEEEEEEEEEE---SSS-BEEEEEEEEEB-TTSEEEEEESS-------------SSB-T---TTEEE
T ss_pred EEEEEEEEecCCCCEEEEEEEEEEC--CCCCcceEEEEEEec-cccEEEEeCCCC------------CeeCC---CCeEE
Confidence 3444444 3478888888888433 899999999999888 222455444411 12221 34444
Q ss_pred EEeecCC-CCC-CCCCccceEEEEEEeecCC
Q 044308 584 VRMPVDS-SEE-DGGEEIDVVCHVKFASQGM 612 (645)
Q Consensus 584 Ar~~~~s-gpa-d~ps~P~~~~aVQFsseGs 612 (645)
-.+.+.+ +.. -......+++.|+|...|.
T Consensus 73 Q~~~v~~~~~~~~~~~~l~~~~~vsy~~~g~ 103 (115)
T PF02883_consen 73 QVIKVENSPFSEPTPKPLKPRLRVSYNVGGQ 103 (115)
T ss_dssp EEEEEEESS-BSTTSSTTEEEEEEEEEETTE
T ss_pred EEEEEEEeecccCCCCCcCeEEEEEEEECCE
Confidence 4443333 210 1124456778999999986
No 12
>TIGR02385 RelE_StbE addiction module toxin, RelE/StbE family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all are found adjacent to RelB/DinJ family antitoxin genes (TIGR02384), as are most genes found by the resulting model. StbE from Morganella morganii plasmid R485 shows typical behaviour for an addiction module toxin. It cannot be cloned without its partner (the antitoxin), whereas its partner cannot confer plasmid stability without StbE.
Probab=51.63 E-value=28 Score=28.36 Aligned_cols=38 Identities=24% Similarity=0.424 Sum_probs=22.3
Q ss_pred ccCCCcccc-ccceeEEeeeceeEEEEEEec--eEEEEEEe
Q 044308 74 SLGDDPLAA-SSGQLIVGVESRYRVVYRLVN--SIYVLGIT 111 (645)
Q Consensus 74 ~~gddpla~-~sG~~vvgv~~~yrv~Yrlvn--~iyvl~vt 111 (645)
.+.+.|+.. ..|.-.+=+..+|||+|++.+ .|+++.|.
T Consensus 42 ~l~~~pl~G~~~g~r~~~v~~~yriiY~i~~~~~I~ii~i~ 82 (88)
T TIGR02385 42 RYRDHPLTGSWKGTRECHIEPDYLLVYQVEEKVVIRLIRVG 82 (88)
T ss_pred cccCccccCCcCCeEEEEECCCEEEEEEECCCcEEEEEecC
Confidence 355666654 345311223338999999987 45555554
No 13
>TIGR02572 LcrR type III secretion system regulator LcrR. This protein is found in type III secretion operons and has been characterized in Yersinia as a regulator of the Low-Calcium Respone (LCR).
Probab=47.44 E-value=63 Score=31.69 Aligned_cols=63 Identities=13% Similarity=0.342 Sum_probs=40.5
Q ss_pred eeceeEEEEEEece-EEEEEEeecCCCCC-CChhHHHHHHhhheeeEEe----------eccccccChhhhhhhh
Q 044308 91 VESRYRVVYRLVNS-IYVLGITNADHDNS-INVFECINIVNQAVSVIVT----------ACRGVDVTPEKLNRKY 153 (645)
Q Consensus 91 v~~~yrv~Yrlvn~-iyvl~vt~a~~~~~-~nvf~~~~~v~~av~V~v~----------~~rGvdvtp~kl~rky 153 (645)
...-|+|+||+=++ |.|+.+--..+..+ .|+|.|+-++..+..-|.. +=||--++-++|.|=|
T Consensus 33 ~l~g~~lawRVE~~rviI~lLrR~~~~~GL~NpFa~LylLae~~~~~lg~~~~lyGnV~vl~gS~ls~~Rl~~FY 107 (139)
T TIGR02572 33 EVDGCELAWRVEEERVWIVLLRRVSQRRGLANPFAALYLLAEAAIALLGPDWRLYGNVDVLAGSPLSSQRLARFY 107 (139)
T ss_pred EEcceEEEEEecCCEEEEEEEEEcccccCcCCcHHHHHHHHHHHHhhcCCCCEEEeeeeEecCCCCcHHHHHHHH
Confidence 34889999999765 44444443332222 4999999999887654433 3445556667776655
No 14
>smart00809 Alpha_adaptinC2 Adaptin C-terminal domain. Adaptins are components of the adaptor complexes which 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. Gamma-adaptin is a subunit of the golgi adaptor. Alpha adaptin is a heterotetramer that regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This Ig-fold domain is found in alpha, beta and gamma adaptins and consists of a beta-sandwich containing 7 strands in 2 beta-sheets in a greek-key topology PUBMED:10430869, PUBMED:12176391. The adaptor appendage contains an additional N-terminal strand.
Probab=37.75 E-value=2.6e+02 Score=23.96 Aligned_cols=86 Identities=16% Similarity=0.408 Sum_probs=47.3
Q ss_pred cEEEEEEeecCceEEEEEEEEeCCCCCCCccceEEEeecCCCCCccccccccccccccceeeEEccCCCCCCCCceEEEE
Q 044308 506 LRVRLIKRHSGTLLSVMVQYVSNPDLPMPLNDVTFSLKLPVDPTLLKVSPKAVLNRSDRELKWIVPEIPVKGAPGKLRVR 585 (645)
Q Consensus 506 L~lr~~wk~~~tlt~V~VdY~yNP~lp~PLtnVq~iL~VPvd~tlLqs~P~A~WN~eerrl~WkLPdIs~~gg~G~LrAr 585 (645)
|++....+..+..++|.+.|.- ..+.+++++++.+.+|-.- .|+.+|... +.|+. + ++..-.
T Consensus 7 l~I~~~~~~~~~~~~i~~~~~N--~s~~~it~f~~~~avpk~~-~l~l~~~s~------------~~l~p-~--~~i~q~ 68 (104)
T smart00809 7 LQIGFKFERRPGLIRITLTFTN--KSPSPITNFSFQAAVPKSL-KLQLQPPSS------------PTLPP-G--GQITQV 68 (104)
T ss_pred EEEEEEEEcCCCeEEEEEEEEe--CCCCeeeeEEEEEEcccce-EEEEcCCCC------------CccCC-C--CCEEEE
Confidence 4444444444566777777743 3458899999999887321 334333321 11221 1 234444
Q ss_pred eecCCCCCCCCCccceEEEEEEeecCC
Q 044308 586 MPVDSSEEDGGEEIDVVCHVKFASQGM 612 (645)
Q Consensus 586 ~~~~sgpad~ps~P~~~~aVQFsseGs 612 (645)
+.+.... +....+++.+.|...|.
T Consensus 69 ~~i~~~~---~~~~~~~~~vsy~~~g~ 92 (104)
T smart00809 69 LKVENPG---KFPLRLRLRLSYLLGGS 92 (104)
T ss_pred EEEECCC---CCCEEEEEEEEEEECCE
Confidence 4444321 34556677888887774
No 15
>PF11353 DUF3153: Protein of unknown function (DUF3153); InterPro: IPR021499 This family of proteins with unknown function appear to be restricted to Cyanobacteria. Some members are annotated as membrane proteins however this cannot be confirmed.
Probab=34.13 E-value=1.2e+02 Score=30.25 Aligned_cols=46 Identities=24% Similarity=0.356 Sum_probs=36.6
Q ss_pred cceEEEeecCCCCCccccccccccccccceeeEEccCCCCCCCCceEEEEe
Q 044308 536 NDVTFSLKLPVDPTLLKVSPKAVLNRSDRELKWIVPEIPVKGAPGKLRVRM 586 (645)
Q Consensus 536 tnVq~iL~VPvd~tlLqs~P~A~WN~eerrl~WkLPdIs~~gg~G~LrAr~ 586 (645)
.|++|.|..|...++.+..|.+.+.. ++++.|+|. .|..-+|.+++
T Consensus 134 ldl~f~l~~P~~~~~~n~~~~~~~~~-~~~l~W~L~----pGe~N~L~~~~ 179 (209)
T PF11353_consen 134 LDLEFSLSTPWGVRSTNGDPNAAEPD-GGQLTWKLQ----PGEINHLEASF 179 (209)
T ss_pred ceEEEEEeCCCcccccCCCCCccccC-CCEEEEecC----CCceeEEEEEE
Confidence 69999999999999988888877655 459999986 23446777776
No 16
>PF10686 DUF2493: Protein of unknown function (DUF2493); InterPro: IPR019627 This entry is represented by Mycobacteriophage D29, Gp61. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this family are mainly Proteobacteria. The function is not known.
Probab=33.65 E-value=28 Score=29.82 Aligned_cols=31 Identities=32% Similarity=0.348 Sum_probs=23.8
Q ss_pred hheeeEEeeccccccChhhhhhhhhHHHHHHHHhHhccc
Q 044308 130 QAVSVIVTACRGVDVTPEKLNRKYAEIYMALDIVLRGVS 168 (645)
Q Consensus 130 ~av~V~v~~~rGvdvtp~kl~rky~evY~ald~vl~g~~ 168 (645)
+..||||+.+| |.+. |.-||.+||.++.-..
T Consensus 2 ~g~rVli~GgR--~~~D------~~~i~~~Ld~~~~~~~ 32 (71)
T PF10686_consen 2 EGMRVLITGGR--DWTD------HELIWAALDKVHARHP 32 (71)
T ss_pred CCCEEEEEECC--cccc------HHHHHHHHHHHHHhCC
Confidence 35699999999 8774 3449999999886553
No 17
>PF06437 ISN1: IMP-specific 5'-nucleotidase; InterPro: IPR009453 The Saccharomyces cerevisiae ISN1 (YOR155c) gene encodes an IMP-specific 5'-nucleotidase, which catalyses degradation of IMP to inosine as part of the purine salvage pathway.; GO: 0000287 magnesium ion binding, 0016791 phosphatase activity, 0009117 nucleotide metabolic process
Probab=27.31 E-value=42 Score=37.64 Aligned_cols=21 Identities=33% Similarity=0.683 Sum_probs=16.8
Q ss_pred cChhhhhhhhhHHHHHHHHhH
Q 044308 144 VTPEKLNRKYAEIYMALDIVL 164 (645)
Q Consensus 144 vtp~kl~rky~evY~ald~vl 164 (645)
.+.+..+|||.||+--++.+.
T Consensus 50 ~~a~~~~~rYaeIf~dvE~lI 70 (408)
T PF06437_consen 50 ATAEEAHRRYAEIFRDVEKLI 70 (408)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 467889999999998776554
No 18
>PF05016 Plasmid_stabil: Plasmid stabilisation system protein; InterPro: IPR007712 Members of this family are involved in plasmid stabilisation. The exact molecular function of this protein is not known.; PDB: 3KXE_A 1WMI_A 3KIQ_y 3KIX_y 2KC9_A 3KHA_B 3KIS_y 3KIU_y 2KC8_A 1Z8M_A ....
Probab=26.28 E-value=1.1e+02 Score=24.89 Aligned_cols=19 Identities=37% Similarity=0.833 Sum_probs=15.1
Q ss_pred eeEEEEEEe--ceEE-EEEEee
Q 044308 94 RYRVVYRLV--NSIY-VLGITN 112 (645)
Q Consensus 94 ~yrv~Yrlv--n~iy-vl~vt~ 112 (645)
.|+|+|++. +.|. |+.|-.
T Consensus 64 ~y~iiY~i~~~~~ii~i~~v~~ 85 (90)
T PF05016_consen 64 DYRIIYRIDEDNDIIYILRVLH 85 (90)
T ss_dssp TEEEEEEEETTTTEEEEEEEEE
T ss_pred eEEEEEEEecCCEEEEEEEEEc
Confidence 999999998 2455 998873
No 19
>PF09621 LcrR: Type III secretion system regulator (LcrR); InterPro: IPR022797 LcrR proteins are encoded within type III secretion operons and have been characterised in Yersinia as a regulator of the Low-Calcium Response (LCR). CesD2 of enteropathogenic Escherichia coli is a chaperone for the Type III Secretion Translocator Protein EspD.
Probab=24.41 E-value=4.5e+02 Score=25.92 Aligned_cols=63 Identities=21% Similarity=0.374 Sum_probs=38.0
Q ss_pred eeceeEEEEEEeceEEEEEEeecCCC-CC-CChhHHHHHHhhheee----------EEeeccccccChhhhhhhh
Q 044308 91 VESRYRVVYRLVNSIYVLGITNADHD-NS-INVFECINIVNQAVSV----------IVTACRGVDVTPEKLNRKY 153 (645)
Q Consensus 91 v~~~yrv~Yrlvn~iyvl~vt~a~~~-~~-~nvf~~~~~v~~av~V----------~v~~~rGvdvtp~kl~rky 153 (645)
...-|+|+||+=.+-.++.--..-+. ++ .|+|.++-++..+..= .|-+-+|=.++.++|.+=|
T Consensus 33 ~l~g~~l~yRvE~~eliIc~lrR~~~~~GL~npFa~L~lLa~~~~~~~~~~~~l~g~Vd~l~~s~l~~~rL~~Fy 107 (139)
T PF09621_consen 33 ELDGYELAYRVEERELIICLLRRVRNNNGLSNPFAALYLLAEATRAVLGPRKVLYGNVDVLRGSPLSSERLAQFY 107 (139)
T ss_pred EEcCeEEEEEecCCEEEEEEEEecCCCcCcCcHHHHHHHHHHHHHHhCCCceEEEEEeeeccCCCccHHHHHHHH
Confidence 56899999999876555544333222 22 4999988777655322 2333444455666666544
Done!