Query 032095
Match_columns 147
No_of_seqs 104 out of 779
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 09:31:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032095.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032095hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01217 Clat_adaptor_s: Clath 100.0 8.9E-39 1.9E-43 231.0 18.4 137 1-143 1-139 (141)
2 COG5030 APS2 Clathrin adaptor 100.0 6.8E-38 1.5E-42 221.3 13.8 135 1-140 1-136 (152)
3 KOG3343 Vesicle coat complex C 100.0 7E-37 1.5E-41 220.5 14.2 140 2-145 9-149 (175)
4 KOG0936 Clathrin adaptor compl 100.0 1.3E-34 2.9E-39 207.5 13.8 142 1-145 1-147 (182)
5 KOG0935 Clathrin adaptor compl 100.0 8.8E-34 1.9E-38 196.0 11.6 137 1-141 1-138 (143)
6 KOG0934 Clathrin adaptor compl 100.0 1.3E-33 2.7E-38 199.2 7.5 133 1-139 1-135 (145)
7 COG5541 RET3 Vesicle coat comp 99.9 7.8E-27 1.7E-31 168.1 9.7 139 2-145 8-155 (187)
8 KOG0938 Adaptor complexes medi 99.9 2.4E-25 5.2E-30 177.9 12.8 137 1-144 1-137 (446)
9 KOG0937 Adaptor complexes medi 99.8 7.5E-19 1.6E-23 144.7 14.1 136 2-142 1-136 (424)
10 KOG2740 Clathrin-associated pr 99.8 1.6E-19 3.4E-24 145.5 9.0 135 1-139 1-135 (418)
11 KOG2635 Medium subunit of clat 99.3 8.9E-11 1.9E-15 97.2 11.8 136 2-143 3-138 (512)
12 PF15001 AP-5_subunit_s1: AP-5 97.7 0.0052 1.1E-07 46.5 15.5 80 57-136 103-182 (189)
13 PF03164 Mon1: Trafficking pro 96.8 0.046 1E-06 46.1 12.8 89 3-95 12-100 (415)
14 PF08923 MAPKK1_Int: Mitogen-a 96.6 0.081 1.8E-06 37.2 11.0 93 2-97 17-115 (119)
15 PF04099 Sybindin: Sybindin-li 87.8 8.2 0.00018 27.7 10.7 96 2-98 1-115 (142)
16 KOG0859 Synaptobrevin/VAMP-lik 87.0 12 0.00026 28.8 11.0 85 10-100 9-93 (217)
17 COG5122 TRS23 Transport protei 85.6 10 0.00022 26.6 10.4 97 2-101 3-109 (134)
18 PF13774 Longin: Regulated-SNA 84.3 8.5 0.00018 24.6 8.2 49 51-99 17-65 (83)
19 KOG0862 Synaptobrevin/VAMP-lik 80.7 24 0.00053 27.3 11.5 100 1-102 1-103 (216)
20 KOG0997 Uncharacterized conser 75.3 54 0.0012 28.6 10.5 84 4-96 119-208 (523)
21 PF03259 Robl_LC7: Roadblock/L 69.0 26 0.00057 22.1 7.9 69 2-72 15-89 (91)
22 COG3322 Predicted periplasmic 60.9 8.2 0.00018 31.3 2.7 21 2-22 104-124 (295)
23 PF08784 RPA_C: Replication pr 49.5 19 0.0004 23.9 2.6 30 102-131 66-99 (102)
24 PF05228 CHASE4: CHASE4 domain 48.6 62 0.0014 22.6 5.5 21 2-22 50-72 (161)
25 PF01535 PPR: PPR repeat; Int 47.6 18 0.00038 17.7 1.8 17 110-126 15-31 (31)
26 PF13812 PPR_3: Pentatricopept 47.6 18 0.00039 18.2 1.9 17 110-126 16-32 (34)
27 PF05184 SapB_1: Saposin-like 44.6 24 0.00052 18.9 2.1 31 85-115 5-35 (39)
28 KOG3369 Transport protein part 42.5 1.5E+02 0.0032 22.5 11.0 48 52-101 125-173 (199)
29 KOG0861 SNARE protein YKT6, sy 41.0 1.6E+02 0.0034 22.4 6.9 88 2-93 3-100 (198)
30 COG2093 DNA-directed RNA polym 35.8 33 0.00072 21.4 1.9 24 124-147 34-59 (64)
31 PF14903 WG_beta_rep: WG conta 32.6 52 0.0011 16.8 2.3 16 7-22 3-18 (35)
32 TIGR00756 PPR pentatricopeptid 31.2 41 0.0009 16.4 1.7 18 110-127 15-32 (35)
33 PF13041 PPR_2: PPR repeat fam 28.9 55 0.0012 18.3 2.1 19 110-128 18-36 (50)
34 KOG0903 Phosphatidylinositol 4 27.8 3.6E+02 0.0078 25.1 7.7 92 27-125 677-787 (847)
35 PF06694 Plant_NMP1: Plant nuc 26.3 1.6E+02 0.0035 24.2 4.9 40 83-122 102-141 (325)
36 PF02268 TFIIA_gamma_N: Transc 25.3 36 0.00078 20.1 0.8 15 114-128 15-29 (49)
37 cd03671 Ap4A_hydrolase_plant_l 24.2 88 0.0019 21.8 2.8 19 4-22 7-25 (147)
38 PF08006 DUF1700: Protein of u 23.4 1.8E+02 0.004 21.2 4.5 50 90-140 6-61 (181)
39 COG3657 Uncharacterized protei 23.4 1E+02 0.0022 20.9 2.8 64 13-76 9-79 (100)
40 PF13998 MgrB: MgrB protein 22.9 61 0.0013 17.0 1.3 16 115-130 3-18 (29)
41 cd03016 PRX_1cys Peroxiredoxin 22.1 1.5E+02 0.0033 22.1 3.9 19 4-22 119-137 (203)
42 cd04685 Nudix_Hydrolase_26 Mem 21.6 1E+02 0.0022 21.4 2.7 18 4-21 4-21 (133)
43 smart00836 DALR_1 DALR anticod 21.6 2.6E+02 0.0055 18.6 5.9 63 76-139 34-97 (122)
44 KOG3368 Transport protein part 20.9 3.3E+02 0.0072 19.6 9.1 83 2-92 3-102 (140)
45 PF02334 RTP: Replication term 20.7 94 0.002 21.7 2.2 34 90-127 37-70 (122)
46 cd04670 Nudix_Hydrolase_12 Mem 20.3 1.3E+02 0.0028 20.1 2.9 18 4-21 6-23 (127)
No 1
>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=100.00 E-value=8.9e-39 Score=230.96 Aligned_cols=137 Identities=26% Similarity=0.445 Sum_probs=116.3
Q ss_pred CceEEEEEeCCCCEEEEecCCC-CHHH-HHHHHHHHHHHhcccCCCCCCccceEEEecCEEEEEEEeCcEEEEEEEcCCC
Q 032095 1 MILAVLFANSEGNILVERFNGV-PAEE-RLHWRSFLVKLGADNLKGVKNEELLVASHKSVYIVYTVLGDVSIFVVGKDEY 78 (147)
Q Consensus 1 MI~~ili~n~~G~~~l~k~Y~~-~~~~-~~~~~~~~~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~e 78 (147)
||+|++|+|++|+++++|||++ +..+ ++.++++.....+ + ++..++++.++++++||++++||+|++++++++
T Consensus 1 MI~~i~i~n~~G~~i~~k~y~~~~~~~~~~~~~~~~~~~~~---~--~~~~~~i~~~~~~~~vy~~~~dl~~~~v~~~~e 75 (141)
T PF01217_consen 1 MIKAILILNSQGKRILSKYYRDVSEEERQKLFEKFIKKKSS---R--NSKQSPIFEHDNYRIVYKRYSDLYFVVVGDENE 75 (141)
T ss_dssp SEEEEEEEETTSEEEEEEESSTSTSHHHHHHHHHHHHHHHT---S--SSSSTSEEEETTEEEEEEEETTEEEEEEESSTS
T ss_pred CEEEEEEEcCCCCEEEehhcCCccHHHHHHHHHHHHHHHHh---c--ccccceeeecccceeeeEeeccEEEEEEeeccc
Confidence 9999999999999999999976 3333 3444444333332 1 223367899999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHHHhHhcCCCCHHHHHhcHHHHHHHHHHHhhCCEEeeeCHHHHHHHHhcCC
Q 032095 79 DELALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLVRLKP 143 (147)
Q Consensus 79 Nel~l~e~l~~~~e~L~~~~~~~v~e~~i~~n~~~v~~lLDEiid~G~i~etd~~~i~~~i~~~~ 143 (147)
||++++++|++++++|+.+|+ ++||+++++||+.+|++||||||+|+|+|||++.|++|++++-
T Consensus 76 Nel~~~e~l~~~v~~l~~~~~-~v~e~~i~~N~~~v~~~LDEiid~G~i~etd~~~I~~~v~~~~ 139 (141)
T PF01217_consen 76 NELLLLEFLHRLVEVLDDYFG-NVSEKDILENFDLVYLILDEIIDGGIILETDPNVILKRVTMQD 139 (141)
T ss_dssp BHHHHHHHHHHHHHHHHHHHS-S-SHHHHHHTHHHHHHHHHHHEETTEES--THHHHHHHHHHCC
T ss_pred chHHHHHHHHHhhhhhhhhhc-cccHHHHHHCHHHHHHHHHHHHhCCEEEECCHHHHHHHHHHhh
Confidence 999999999999999999998 6999999999999999999999999999999999999998863
No 2
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=100.00 E-value=6.8e-38 Score=221.27 Aligned_cols=135 Identities=19% Similarity=0.215 Sum_probs=121.8
Q ss_pred CceEEEEEeCCCCEEEEecCCC-CHHHHHHHHHHHHHHhcccCCCCCCccceEEEecCEEEEEEEeCcEEEEEEEcCCCC
Q 032095 1 MILAVLFANSEGNILVERFNGV-PAEERLHWRSFLVKLGADNLKGVKNEELLVASHKSVYIVYTVLGDVSIFVVGKDEYD 79 (147)
Q Consensus 1 MI~~ili~n~~G~~~l~k~Y~~-~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eN 79 (147)
||++++|+|++|++|++|||.| +.++|+.+.+.+++++. + |.++++ .+.+..+.++|||||++|||+.+.++++|
T Consensus 1 ~i~~vli~nrqgk~RL~K~yt~~~~~e~~kli~~i~~lIs-~-R~~ke~--N~~e~k~~kiVYrrYA~LyF~f~Vd~~dn 76 (152)
T COG5030 1 MIKFVLIFNRQGKPRLVKWYTPVSDPEQAKLIADIYELIS-A-RKPKES--NFIEGKNEKIVYRRYATLYFVFGVDNDDN 76 (152)
T ss_pred CeEEEEEEcCCCceeeeEeeccCCcHHHHHHHHHHHHHHH-c-CCchhc--ccccccCcEEEeeecCcEEEEEEEcCCCC
Confidence 8999999999999999999998 67778888888888663 2 222333 38888889999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhHhcCCCCHHHHHhcHHHHHHHHHHHhhCCEEeeeCHHHHHHHHh
Q 032095 80 ELALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLVR 140 (147)
Q Consensus 80 el~l~e~l~~~~e~L~~~~~~~v~e~~i~~n~~~v~~lLDEiid~G~i~etd~~~i~~~i~ 140 (147)
||+++++||.|+|+|+.+|| +|||+|+++||.++|.+||||+.+|.++|+++..+++++.
T Consensus 77 El~iL~lIh~FVE~lDr~Fg-nVCELdlIFNF~kv~~ILdE~i~gG~i~Es~~~~vl~~v~ 136 (152)
T COG5030 77 ELIILELIHNFVEILDRFFG-NVCELDLIFNFQKVYAILDEMILGGEIIESSKNEVLEHVY 136 (152)
T ss_pred cchHHHHHHHHHHHHHHHhc-cceeeEeEeeHHHHHHHHHHHHhCCeeeecCHHHHHHHHH
Confidence 99999999999999999997 6999999999999999999999999999999999998874
No 3
>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=7e-37 Score=220.50 Aligned_cols=140 Identities=26% Similarity=0.374 Sum_probs=128.3
Q ss_pred ceEEEEEeCCCCEEEEecCCCCHHH-HHHHHHHHHHHhcccCCCCCCccceEEEecCEEEEEEEeCcEEEEEEEcCCCCH
Q 032095 2 ILAVLFANSEGNILVERFNGVPAEE-RLHWRSFLVKLGADNLKGVKNEELLVASHKSVYIVYTVLGDVSIFVVGKDEYDE 80 (147)
Q Consensus 2 I~~ili~n~~G~~~l~k~Y~~~~~~-~~~~~~~~~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNe 80 (147)
++|++|+|++|+|+++|||+++... -+.+.+|++.+++|++|+ +..|..++|..+|||.+-||+|+++|+.+|||
T Consensus 9 vk~iliLD~~G~Ri~aKYY~~~~~s~vkeqkaFEK~lF~KT~kt----~~eI~~ldg~~vvYk~~~Dl~fyv~G~~~ENE 84 (175)
T KOG3343|consen 9 VKAILILDSDGKRILAKYYDDPHPSTVKEQKAFEKNLFSKTSKT----ESEILLLDGNTVVYKSVIDLHFYVVGSEEENE 84 (175)
T ss_pred hheEEEEcCCCCEeeeeecCCCcchhHHHHHHHHHHHhcccccc----cceeEEecCcEEEEEecccEEEEEecCcchhH
Confidence 6899999999999999999985443 567788888899888664 33499999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhHhcCCCCHHHHHhcHHHHHHHHHHHhhCCEEeeeCHHHHHHHHhcCCCC
Q 032095 81 LALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLVRLKPPN 145 (147)
Q Consensus 81 l~l~e~l~~~~e~L~~~~~~~v~e~~i~~n~~~v~~lLDEiid~G~i~etd~~~i~~~i~~~~~~ 145 (147)
+.+.++++++.++++..+++|++++.+++|+|.+++++|||||+|+|+||||+.|+.|+..+|..
T Consensus 85 l~L~svL~~l~dal~llLr~nveKr~llEN~D~i~L~~DEiiD~GvILEtdp~~ia~rv~~~~~~ 149 (175)
T KOG3343|consen 85 LMLMSVLTCLFDALSLLLRKNVEKRELLENLDLIFLALDEIIDGGVILETDPNQIAQRVALRPTD 149 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHhChhHHHHHhhhccceeehhhhccCceEEecCHHHHHHHhccCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999766654
No 4
>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.3e-34 Score=207.48 Aligned_cols=142 Identities=18% Similarity=0.171 Sum_probs=118.2
Q ss_pred CceEEEEEeCCCCEEEEecCCC-CHHHHHHHHHHHHHHhcccCCCCCCcc----ceEEEecCEEEEEEEeCcEEEEEEEc
Q 032095 1 MILAVLFANSEGNILVERFNGV-PAEERLHWRSFLVKLGADNLKGVKNEE----LLVASHKSVYIVYTVLGDVSIFVVGK 75 (147)
Q Consensus 1 MI~~ili~n~~G~~~l~k~Y~~-~~~~~~~~~~~~~~i~~~~~~~~~~~~----~~i~~~~~~~ivy~~~~dl~~~~v~~ 75 (147)
||+|++|+|++|++|++|||++ +.+.|+.+.+....+..+ |...-|+ ...+--.+.+++||+|+.|||+.|.+
T Consensus 1 MI~AvlifNn~gkPRL~KFY~p~~~~~Qq~lir~vf~lvs~--R~~n~~nFLe~~~l~g~~d~rlIYrhYATLYFvfvvD 78 (182)
T KOG0936|consen 1 MIKAVLIFNNKGKPRLVKFYTPVDEEKQQQLIREVFHLVSK--RPDNVCNFLEGNSLIGGSDNRLIYRHYATLYFVFVVD 78 (182)
T ss_pred CeeEEEEecCCCCcceeeecCcCChHHHHHHHHHHHHHHHc--CCchHhhhhccccccCCccceeehheeeeEEEEEEEc
Confidence 9999999999999999999999 666565555555554422 2222121 11221237999999999999999999
Q ss_pred CCCCHHHHHHHHHHHHHHHHhHhcCCCCHHHHHhcHHHHHHHHHHHhhCCEEeeeCHHHHHHHHhcCCCC
Q 032095 76 DEYDELALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLVRLKPPN 145 (147)
Q Consensus 76 ~~eNel~l~e~l~~~~e~L~~~~~~~v~e~~i~~n~~~v~~lLDEiid~G~i~etd~~~i~~~i~~~~~~ 145 (147)
++|+||+++++||.|+|+|++.|. ++||.|+++|++++|.+|+|++.||.++||+.+.|...+..+.+-
T Consensus 79 ~sEsEL~iLDLIQvfVEtLDkCF~-nVcELDliF~~~k~h~iL~EiV~GGmVlETn~neIv~av~~~nkl 147 (182)
T KOG0936|consen 79 SSESELGILDLIQVFVETLDKCFE-NVCELDLIFNWQKVHAILAEIVMGGMVLETNMNEIVAAVDEQNKL 147 (182)
T ss_pred CCcchhHHHHHHHHHHHHHHHHHH-hhhhhhheeeHHHHHHHHHHHHhCCeEEeccHHHHHHHHHHhchh
Confidence 999999999999999999999885 799999999999999999999999999999999999998877654
No 5
>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=8.8e-34 Score=196.05 Aligned_cols=137 Identities=16% Similarity=0.149 Sum_probs=116.9
Q ss_pred CceEEEEEeCCCCEEEEecCCC-CHHHHHHHHHHHHHHhcccCCCCCCccceEEEecCEEEEEEEeCcEEEEEEEcCCCC
Q 032095 1 MILAVLFANSEGNILVERFNGV-PAEERLHWRSFLVKLGADNLKGVKNEELLVASHKSVYIVYTVLGDVSIFVVGKDEYD 79 (147)
Q Consensus 1 MI~~ili~n~~G~~~l~k~Y~~-~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eN 79 (147)
||.+|+|.|++|++|++|||.+ +..+++......++++.. |..+- +..+.......+.+|+|++|||+.+.+..+|
T Consensus 1 mi~FILiqNr~Gk~RLak~yv~~dd~ek~~~~~~vh~lvs~--Rd~K~-~~~~~~~~~~~~~~rryagLyf~~~vd~tDn 77 (143)
T KOG0935|consen 1 MIRFILIQNRAGKTRLAKWYVQFDDDEKQKLIEEVHALVTV--RDAKH-TNFVEFRNFKIIYRRRYAGLYFCICVDVTDN 77 (143)
T ss_pred CeEEEEEEccccceeheeeeeccCchHHHHHHHHHHHHHhh--ccchh-hhheeeeeceEEEEEeeCCEEEEEEEecCCc
Confidence 9999999999999999999998 445566777777776631 22221 2234445556666679999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhHhcCCCCHHHHHhcHHHHHHHHHHHhhCCEEeeeCHHHHHHHHhc
Q 032095 80 ELALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLVRL 141 (147)
Q Consensus 80 el~l~e~l~~~~e~L~~~~~~~v~e~~i~~n~~~v~~lLDEiid~G~i~etd~~~i~~~i~~ 141 (147)
|++.++.||.|+|+|+.+|+ |+||.|+++||.+||.++|||+-+|.++||++..+++|+.+
T Consensus 78 elayLe~IHlFVEvLd~fF~-NVCELDlvFNFyKVy~i~DEm~l~GEi~Etsk~~vlerl~~ 138 (143)
T KOG0935|consen 78 ELAYLEHIHLFVEVLDEFFH-NVCELDLVFNFYKVYTIVDEMFLAGEIRETSKTKVLERLLM 138 (143)
T ss_pred hHHHHHHHHHHHHHHHHHhc-cccceeeeeeeeeHHHHHHHHHHhhhhhhhhHHHHHHHHHH
Confidence 99999999999999999997 69999999999999999999999999999999999999975
No 6
>KOG0934 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.3e-33 Score=199.19 Aligned_cols=133 Identities=22% Similarity=0.270 Sum_probs=117.4
Q ss_pred CceEEEEEeCCCCEEEEecCCC-CHHHHHHHHHHHHH-HhcccCCCCCCccceEEEecCEEEEEEEeCcEEEEEEEcCCC
Q 032095 1 MILAVLFANSEGNILVERFNGV-PAEERLHWRSFLVK-LGADNLKGVKNEELLVASHKSVYIVYTVLGDVSIFVVGKDEY 78 (147)
Q Consensus 1 MI~~ili~n~~G~~~l~k~Y~~-~~~~~~~~~~~~~~-i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~e 78 (147)
||+++++.+++|+.|++|||.+ +..+|+.+++.+.+ +.+ |.++.|+ +++++++++|||||++|+|++...+++
T Consensus 1 mi~f~LlvsrQGk~rL~k~y~~~~~~er~~i~re~i~~~La---r~pk~cs--fie~kd~kvVyrryasl~f~~~v~~~d 75 (145)
T KOG0934|consen 1 MIKFFLLVSRQGKTRLQKWYEALSIKERKKIERELIKSVLA---RKPKMCS--FIEYKDEKVVYRRYASLFFCVGVEDND 75 (145)
T ss_pred CeEEEEEEeccCceehhHHHhhhcHHHHHHHHHHHHHHHHh---CCccccc--chhccCceehhhhhhhEEEEEEEecCC
Confidence 8999999999999999999998 77777776666544 332 3334444 889999999999999998888888999
Q ss_pred CHHHHHHHHHHHHHHHHhHhcCCCCHHHHHhcHHHHHHHHHHHhhCCEEeeeCHHHHHHHH
Q 032095 79 DELALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLV 139 (147)
Q Consensus 79 Nel~l~e~l~~~~e~L~~~~~~~v~e~~i~~n~~~v~~lLDEiid~G~i~etd~~~i~~~i 139 (147)
|||+++|+||.++|+|++||| +|||+|+++||.++|.+|||++-+|-++|+.++.....+
T Consensus 76 NEL~~LE~IH~~vE~lDkYFg-~VCELDiiFNfekay~ILde~~~~g~~~e~~k~~~~~~i 135 (145)
T KOG0934|consen 76 NELAILEFIHNYVELLDKYFG-SVCELDIIFNFEKAYFILDEFLLGGEIQETSKNDVLKAI 135 (145)
T ss_pred chhhHHHHHHHHHHHHHHHhc-cceeeEEEEehHhHHHHHHHHhcCcchHhhhcccHHHHH
Confidence 999999999999999999997 699999999999999999999999999999998877776
No 7
>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=7.8e-27 Score=168.13 Aligned_cols=139 Identities=24% Similarity=0.333 Sum_probs=123.6
Q ss_pred ceEEEEEeCCCCEEEEecCCCCHHH---------HHHHHHHHHHHhcccCCCCCCccceEEEecCEEEEEEEeCcEEEEE
Q 032095 2 ILAVLFANSEGNILVERFNGVPAEE---------RLHWRSFLVKLGADNLKGVKNEELLVASHKSVYIVYTVLGDVSIFV 72 (147)
Q Consensus 2 I~~ili~n~~G~~~l~k~Y~~~~~~---------~~~~~~~~~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~ 72 (147)
+.|++|+|++|++++.|||.|++.. -+..+.|++++.+++++..+ .|..+.++.++|+++-|+.+++
T Consensus 8 v~a~LilDsqGeriy~kyy~pph~~eg~~~vFnsvkkekefek~l~eKt~k~~~----~Il~f~d~lV~~k~~~dv~~yi 83 (187)
T COG5541 8 VEALLILDSQGERIYRKYYQPPHRSEGHQLVFNSVKKEKEFEKKLAEKTAKDRE----SILMFYDRLVMCKRLDDVLLYI 83 (187)
T ss_pred eeeeEEecCCccchhhhhcCCcccccccchhhcchhHHHHHHHHHHHHhhcCcc----ceeeEcceeeeeeeehhEEEEE
Confidence 6899999999999999999985321 13456677778877766533 3888999999999999999999
Q ss_pred EEcCCCCHHHHHHHHHHHHHHHHhHhcCCCCHHHHHhcHHHHHHHHHHHhhCCEEeeeCHHHHHHHHhcCCCC
Q 032095 73 VGKDEYDELALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLVRLKPPN 145 (147)
Q Consensus 73 v~~~~eNel~l~e~l~~~~e~L~~~~~~~v~e~~i~~n~~~v~~lLDEiid~G~i~etd~~~i~~~i~~~~~~ 145 (147)
+++-++||..+.+.+..+..+|..+++...+++.+.+|||.+.+++||.||+|+|+||+++.|+.|+ .|||+
T Consensus 84 v~~meeNE~~l~q~f~~ir~Al~li~k~~~dkr~v~enYDqivl~vdEtid~Gvilet~s~~ia~rv-~K~p~ 155 (187)
T COG5541 84 VSPMEENEPFLGQVFDEIRAALILIVKTPTDKRNVWENYDQIVLLVDETIDEGVILETKSDEIADRV-PKPPN 155 (187)
T ss_pred ecccccccHHHHHHHHHHHHHHHHHHcCCcchhhHHhhhceEEEeeehhcccceEeecChHHHHHhC-CCCCC
Confidence 9999999999999999999999999998888999999999999999999999999999999999999 67765
No 8
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.93 E-value=2.4e-25 Score=177.86 Aligned_cols=137 Identities=18% Similarity=0.195 Sum_probs=127.4
Q ss_pred CceEEEEEeCCCCEEEEecCCCCHHHHHHHHHHHHHHhcccCCCCCCccceEEEecCEEEEEEEeCcEEEEEEEcCCCCH
Q 032095 1 MILAVLFANSEGNILVERFNGVPAEERLHWRSFLVKLGADNLKGVKNEELLVASHKSVYIVYTVLGDVSIFVVGKDEYDE 80 (147)
Q Consensus 1 MI~~ili~n~~G~~~l~k~Y~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNe 80 (147)
||+|++|+|.+|++++.|.|+.+.. |+.-+.|..+++. + .+.++|+...+++.++|.+..|||+++++.+|.|-
T Consensus 1 misglfi~n~rGevlink~fr~dlk-rs~~diFRv~vi~-n----~d~r~PV~~igsttf~~~r~~nl~lvaitksN~Nv 74 (446)
T KOG0938|consen 1 MISGLFIYNLRGEVLINKTFRDDLK-RSIVDIFRVQVIN-N----LDVRSPVLTIGSTTFHHIRSSNLWLVAITKSNANV 74 (446)
T ss_pred CcceEEEEeccCcEEEehhhhhhhh-hhHHHHHHHhhhh-c----cccCCCeeEecceeEEEEeeccEEEEEEecCCCch
Confidence 9999999999999999999999654 7788888888883 2 45678999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhHhcCCCCHHHHHhcHHHHHHHHHHHhhCCEEeeeCHHHHHHHHhcCCC
Q 032095 81 LALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLVRLKPP 144 (147)
Q Consensus 81 l~l~e~l~~~~e~L~~~~~~~v~e~~i~~n~~~v~~lLDEiid~G~i~etd~~~i~~~i~~~~~ 144 (147)
.+++||+..+.+++..||| ..+|..+.+||..+|++||||+|.|+|++|+|+.++..++.++.
T Consensus 75 a~v~eFl~kl~avm~aYfg-k~~Eeaiknnf~lI~ElLDemld~G~pqnte~~al~~~is~~~V 137 (446)
T KOG0938|consen 75 AAVFEFLYKLDAVMNAYFG-KDREEAIKNNFVLIYELLDEMLDFGIPQNTEPNALKAQISQKGV 137 (446)
T ss_pred hhHHHHHHHHHHHHHHHhc-ccchhhhhhceEeHHHHHHHHHhcCCCccCChhHHHhhhhhhhh
Confidence 9999999999999999998 49999999999999999999999999999999999999987764
No 9
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.81 E-value=7.5e-19 Score=144.67 Aligned_cols=136 Identities=15% Similarity=0.164 Sum_probs=122.7
Q ss_pred ceEEEEEeCCCCEEEEecCCCCHHHHHHHHHHHHHHhcccCCCCCCccceEEEecCEEEEEEEeCcEEEEEEEcCCCCHH
Q 032095 2 ILAVLFANSEGNILVERFNGVPAEERLHWRSFLVKLGADNLKGVKNEELLVASHKSVYIVYTVLGDVSIFVVGKDEYDEL 81 (147)
Q Consensus 2 I~~ili~n~~G~~~l~k~Y~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNel 81 (147)
+++++++|.+|+++++|-|+.+. .....++|...++.+ ...+..+|++.++|..++|.++.+||+++.+..|.|..
T Consensus 1 ~sa~fild~~G~~lisr~yr~dv-~~s~~~~F~~~l~~~---e~~~~~~p~l~~~g~~~~~ik~s~lylv~~~~~n~~a~ 76 (424)
T KOG0937|consen 1 ASAVFILDHKGEVLISRDYRGDV-PMSSTEKFFRKLFEK---EEGDESPPFLVHDGSRFIHIKHSNLYLVAGTRPNVSAA 76 (424)
T ss_pred CceEEEEcCCCcEeEeecccccC-ChhhhhhHHHHHhhh---cccCCCCCeEEeCCceEEEEeecceEEEEEeccCCCHH
Confidence 57999999999999999999853 366778888665532 23456778999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhHhcCCCCHHHHHhcHHHHHHHHHHHhhCCEEeeeCHHHHHHHHhcC
Q 032095 82 ALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLVRLK 142 (147)
Q Consensus 82 ~l~e~l~~~~e~L~~~~~~~v~e~~i~~n~~~v~~lLDEiid~G~i~etd~~~i~~~i~~~ 142 (147)
.++++++++++++.+||+ .+.|..+.+|+..+|++|||++|.|++|.|+++.+.+.+.++
T Consensus 77 ~v~~~l~~~~~v~~~y~~-~l~e~si~~n~vlvyElLde~mDFGypQ~t~s~iL~~yi~~~ 136 (424)
T KOG0937|consen 77 LVLSFLYAVADVFGDYLS-ELEEESIRDNFVLVYELLDEVMDFGYPQTTDSEILKNYITQK 136 (424)
T ss_pred HHHHHHHHHHHHHHHHhc-cCCccceecchHHHHHHHHHHhccCCcccchHHHHHHHhccc
Confidence 999999999999999998 599999999999999999999999999999999999999887
No 10
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.80 E-value=1.6e-19 Score=145.47 Aligned_cols=135 Identities=19% Similarity=0.218 Sum_probs=109.6
Q ss_pred CceEEEEEeCCCCEEEEecCCCCHHHHHHHHHHHHHHhcccCCCCCCccceEEEecCEEEEEEEeCcEEEEEEEcCCCCH
Q 032095 1 MILAVLFANSEGNILVERFNGVPAEERLHWRSFLVKLGADNLKGVKNEELLVASHKSVYIVYTVLGDVSIFVVGKDEYDE 80 (147)
Q Consensus 1 MI~~ili~n~~G~~~l~k~Y~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNe 80 (147)
||+++++.|.+|+.++.|.++...-.|+...-|+..-. +. ...+..+|++....+++.-.-..++++++++..+..+
T Consensus 1 mi~siflidtsg~l~lek~~~g~t~~rsic~~f~e~~~-~~--~~~e~~ppvi~~p~hylfsv~~~~i~~~~~st~e~pP 77 (418)
T KOG2740|consen 1 MILSIFLIDTSGDLLLEKHLKGSTVVRSICDYFFEDQS-SD--DDLEHVPPVISTPHHYLFSVYRDLIFFCAVSTVETPP 77 (418)
T ss_pred CeeEEEEEcCCchhhhhHhhCCceeeeehHHHHHHhhh-hc--cccccCCceecCCceeeeeeeccCcEEEEEEeccCCC
Confidence 99999999999999999999974444555554444333 21 2234455666565566665556677778888878889
Q ss_pred HHHHHHHHHHHHHHHhHhcCCCCHHHHHhcHHHHHHHHHHHhhCCEEeeeCHHHHHHHH
Q 032095 81 LALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLV 139 (147)
Q Consensus 81 l~l~e~l~~~~e~L~~~~~~~v~e~~i~~n~~~v~~lLDEiid~G~i~etd~~~i~~~i 139 (147)
|.+.|||+++++++..|||+ .++..+.+|+..||++||||+|+|++..||++.+++.|
T Consensus 78 L~~iefL~rv~dv~~eyFg~-~s~~~Ik~N~~vv~ell~emiDnGfpl~tE~NiLke~i 135 (418)
T KOG2740|consen 78 LMVIEFLHRVVDVLLEYFGG-LSESKIKDNVVVVYELLDEMIDNGFPLVTEPNILKELI 135 (418)
T ss_pred hhHHHHHHHHHHHHHHHhcc-cCHhHhhcceeeHHHHHHHHHHcCCCcccChhHHHhhc
Confidence 99999999999999999985 99999999999999999999999999999999998887
No 11
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.25 E-value=8.9e-11 Score=97.20 Aligned_cols=136 Identities=19% Similarity=0.264 Sum_probs=118.4
Q ss_pred ceEEEEEeCCCCEEEEecCCCCHHHHHHHHHHHHHHhcccCCCCCCccceEEEecCEEEEEEEeCcEEEEEEEcCCCCHH
Q 032095 2 ILAVLFANSEGNILVERFNGVPAEERLHWRSFLVKLGADNLKGVKNEELLVASHKSVYIVYTVLGDVSIFVVGKDEYDEL 81 (147)
Q Consensus 2 I~~ili~n~~G~~~l~k~Y~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNel 81 (147)
+-+..+.+++|+.+++|.|+. -.|.+++.++....+ - -+ ...++.+++-+.+++||+...++|++++++.+.|-|
T Consensus 3 vlaa~i~t~~Gk~ivsRqf~~--Msr~RIEgLl~aFpk-L-v~-~~~qhT~vEt~~VRYVYqP~d~lY~vLITtk~SNIl 77 (512)
T KOG2635|consen 3 VLAASINTKTGKAIVSRQFRE--MSRSRIEGLLAAFPK-L-VS-AGKQHTFVETDSVRYVYQPLDNLYIVLITTKQSNIL 77 (512)
T ss_pred EEEEEEeecCCceeeehHhHh--hhHHHHHHHHHHhHH-h-hc-cCCCccEEecccEEEEEEecccEEEEEEeccccchh
Confidence 567788899999999999995 347778877766542 1 11 124567889999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhHhcCCCCHHHHHhcHHHHHHHHHHHhhCCEEeeeCHHHHHHHHhcCC
Q 032095 82 ALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIRRLVRLKP 143 (147)
Q Consensus 82 ~l~e~l~~~~e~L~~~~~~~v~e~~i~~n~~~v~~lLDEiid~G~i~etd~~~i~~~i~~~~ 143 (147)
--++.|+.|..+...||. .++|+.+.+|-..+...+||++.-||-.+++...|+....|.+
T Consensus 78 eDl~TL~Lfskvipey~~-slde~eI~~~~FelifAFDEivsLGyre~v~laQikty~eMdS 138 (512)
T KOG2635|consen 78 EDLETLRLFSKVIPEYCS-SLDEKEILENAFELIFAFDEIVSLGYRENVNLAQIKTYLEMDS 138 (512)
T ss_pred hHHHHHHHHHHhchhhhh-hhhHHHHHHhhhhhhhccchhhhhcccccccHHHhhhhhcccc
Confidence 999999999999999997 6999999999999999999999999999999999999988765
No 12
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=97.73 E-value=0.0052 Score=46.51 Aligned_cols=80 Identities=13% Similarity=0.118 Sum_probs=70.0
Q ss_pred CEEEEEEEeCcEEEEEEEcCCCCHHHHHHHHHHHHHHHHhHhcCCCCHHHHHhcHHHHHHHHHHHhhCCEEeeeCHHHHH
Q 032095 57 SVYIVYTVLGDVSIFVVGKDEYDELALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTEKDRIR 136 (147)
Q Consensus 57 ~~~ivy~~~~dl~~~~v~~~~eNel~l~e~l~~~~e~L~~~~~~~v~e~~i~~n~~~v~~lLDEiid~G~i~etd~~~i~ 136 (147)
...++|...+++.|.+|.++.||-++.-.+|+.++..|.+.++.-..-..++.+-|.+..+|+..+-.|-.+=.|.+.++
T Consensus 103 ~k~vvW~~v~~l~ftLVce~hEN~lLa~~~L~~~~~~l~~~~~~l~~~~e~l~k~d~i~aiL~~fLP~GQLLFlN~~~~k 182 (189)
T PF15001_consen 103 PKIVVWLGVGSLCFTLVCEPHENRLLAENTLRLFIRHLLEHLKILSQPSEVLLKSDRILAILHRFLPHGQLLFLNHRFVK 182 (189)
T ss_pred CcEEEeeccCCEEEEEEecCchhHHHHHHHHHHHHHHHHHHHHHhCcHHHhhhhHHHHHHHHHHhCCCCcEEEEcHHHHH
Confidence 47899999999999999999999999999999999999888853233366788999999999999999988888877654
No 13
>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=96.77 E-value=0.046 Score=46.12 Aligned_cols=89 Identities=15% Similarity=0.109 Sum_probs=58.2
Q ss_pred eEEEEEeCCCCEEEEecCCCCHHHHHHHHHHHHHHhcccCCCCCCccceEEEecCEEEEEEEeCcEEEEEEEcCCCCHHH
Q 032095 3 LAVLFANSEGNILVERFNGVPAEERLHWRSFLVKLGADNLKGVKNEELLVASHKSVYIVYTVLGDVSIFVVGKDEYDELA 82 (147)
Q Consensus 3 ~~ili~n~~G~~~l~k~Y~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNel~ 82 (147)
+-+||+++.||++++|| ++...-..+-..+..++.-- .... ...--+..+++++|+-..+-|+++++++.+|++-.
T Consensus 12 kh~fIlS~AGKPIysr~--G~e~~l~~~~g~~~aiiS~~-~~~~-d~l~~i~~~~~~ivfl~r~pl~lv~vS~~~e~~~~ 87 (415)
T PF03164_consen 12 KHFFILSSAGKPIYSRY--GDEDKLSSLMGVIQAIISFF-QSNG-DELRSIRAGDHRIVFLNRGPLILVAVSKTGESESQ 87 (415)
T ss_pred CeEEEECCCCceeEEec--CChHHHHHHHHHHHHHHHHH-HhCC-CcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCHHH
Confidence 34799999999999999 32232333333444433211 1111 22224457899999999999999999999999877
Q ss_pred HHHHHHHHHHHHH
Q 032095 83 LAEVIFAITSAVK 95 (147)
Q Consensus 83 l~e~l~~~~e~L~ 95 (147)
+..-|+.++.-+-
T Consensus 88 l~~qL~~ly~qil 100 (415)
T PF03164_consen 88 LRKQLDYLYSQIL 100 (415)
T ss_pred HHHHHHHHHHHHH
Confidence 7666655554433
No 14
>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=96.57 E-value=0.081 Score=37.21 Aligned_cols=93 Identities=9% Similarity=0.066 Sum_probs=63.1
Q ss_pred ceEEEEEeCCCCEEEEecCCCCH--HHHHH----HHHHHHHHhcccCCCCCCccceEEEecCEEEEEEEeCcEEEEEEEc
Q 032095 2 ILAVLFANSEGNILVERFNGVPA--EERLH----WRSFLVKLGADNLKGVKNEELLVASHKSVYIVYTVLGDVSIFVVGK 75 (147)
Q Consensus 2 I~~ili~n~~G~~~l~k~Y~~~~--~~~~~----~~~~~~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~ 75 (147)
+.+|+|.|++|-+++.=...... .-|.. +-....|.. | +.- .....-+..++++.++.-....+++.++++
T Consensus 17 l~~I~itDrDGvpi~~v~~~~~~~~~~~~~~~~tf~~a~~Q~~-K-L~l-G~nk~ii~~Y~~~qvv~~~~~pl~it~ias 93 (119)
T PF08923_consen 17 LQAIVITDRDGVPIAKVSSDSAPESAMRPSLLSTFAMAIDQAS-K-LGL-GKNKSIIAYYDSYQVVQFNKLPLYITFIAS 93 (119)
T ss_dssp EEEEEEEETTS-EEEEEE-TTS-GGGGSHHHHCCHHHHHHHHT-T-SSS--SEEEEEEEESSEEEEEEEETTEEEEEEEE
T ss_pred eEEEEEECCCCcEEEEecCCCCcchhhhhHHHHHHHHHhhccc-c-cCC-CCceEEEEEeCCEEEEEEeCCCeEEEEEec
Confidence 57999999999998885555421 11111 122223332 1 111 223445788999999999999999999999
Q ss_pred CCCCHHHHHHHHHHHHHHHHhH
Q 032095 76 DEYDELALAEVIFAITSAVKDA 97 (147)
Q Consensus 76 ~~eNel~l~e~l~~~~e~L~~~ 97 (147)
++.|-=+++.+=+.+...+...
T Consensus 94 ~~aN~G~il~l~~~L~~~l~~l 115 (119)
T PF08923_consen 94 SNANTGLILSLEEELAPILNEL 115 (119)
T ss_dssp TTS-HHHHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHhHHHHHHHHHHH
Confidence 9999999999888888888764
No 15
>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=87.77 E-value=8.2 Score=27.67 Aligned_cols=96 Identities=11% Similarity=0.070 Sum_probs=52.3
Q ss_pred ceEEEEEeCCCCEEEEecCCCCH---------HHHHHHHHHH-------HHHhcccCCCC--CCccceEEEecCEEEE-E
Q 032095 2 ILAVLFANSEGNILVERFNGVPA---------EERLHWRSFL-------VKLGADNLKGV--KNEELLVASHKSVYIV-Y 62 (147)
Q Consensus 2 I~~ili~n~~G~~~l~k~Y~~~~---------~~~~~~~~~~-------~~i~~~~~~~~--~~~~~~i~~~~~~~iv-y 62 (147)
|..+.|+|+.|.-++.|-|.... +++..+-..+ .++.....+.. ..+.-.-+..+.+++- |
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 67899999999999999998622 2332222222 22221110100 0111223445566554 4
Q ss_pred EEeCcEEEEEEEcCCCCHHHHHHHHHHHHHHHHhHh
Q 032095 63 TVLGDVSIFVVGKDEYDELALAEVIFAITSAVKDAC 98 (147)
Q Consensus 63 ~~~~dl~~~~v~~~~eNel~l~e~l~~~~e~L~~~~ 98 (147)
..-.++-|+++++.+... ..-++++.+.++..+|.
T Consensus 81 eT~TGlKFvl~td~~~~~-~~~~l~~~~~~lY~dyV 115 (142)
T PF04099_consen 81 ETPTGLKFVLITDPNVPS-LRDELLRIYYELYVDYV 115 (142)
T ss_dssp E-TTS-EEEEEE-TTCCH-CHHHHHHHHHHHHHHHH
T ss_pred EcCcCcEEEEEecCCCcc-HHHHHHHHHHHHHHHHH
Confidence 568889999999988754 34556778888877765
No 16
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=87.03 E-value=12 Score=28.76 Aligned_cols=85 Identities=12% Similarity=0.139 Sum_probs=57.6
Q ss_pred CCCCEEEEecCCCCHHHHHHHHHHHHHHhcccCCCCCCccceEEEecCEEEEEEEeCcEEEEEEEcCCCCHHHHHHHHHH
Q 032095 10 SEGNILVERFNGVPAEERLHWRSFLVKLGADNLKGVKNEELLVASHKSVYIVYTVLGDVSIFVVGKDEYDELALAEVIFA 89 (147)
Q Consensus 10 ~~G~~~l~k~Y~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~eNel~l~e~l~~ 89 (147)
.+|-+++++|=.-+.. -..+-++.-+.+ .+. +.+.....+|+|.+-|.+-+++.++++++++..--.-+.||..
T Consensus 9 ARGTvvLaeft~~~gN-f~sva~qiL~kl----p~~-~n~k~tYs~d~y~Fh~l~~dg~tylcvadds~gR~ipfaFLe~ 82 (217)
T KOG0859|consen 9 ARGTVILAEFTEFSGN-FSSIAAQILQKL----PSS-SNSKFTYSCDGYTFHYLVEDGLTYLCVADDSAGRQIPFAFLER 82 (217)
T ss_pred ecceEEEEeeeeccCC-HHHHHHHHHHhC----CCC-CCCceEEecCCeEEEEEEeCCeEEEEEEeccccccccHHHHHH
Confidence 6899999998765222 112222322222 221 2223456789999999999999999999998777777777777
Q ss_pred HHHHHHhHhcC
Q 032095 90 ITSAVKDACGK 100 (147)
Q Consensus 90 ~~e~L~~~~~~ 100 (147)
+-+-+.+-.|+
T Consensus 83 Ik~~F~k~YG~ 93 (217)
T KOG0859|consen 83 IKEDFKKRYGG 93 (217)
T ss_pred HHHHHHHHhcc
Confidence 77777666665
No 17
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=85.65 E-value=10 Score=26.61 Aligned_cols=97 Identities=16% Similarity=0.142 Sum_probs=56.9
Q ss_pred ceEEEEEeCCCCEEEEecCCCCHHHHHH-----HHHHHHH---HhcccCCCCCCccceEEEecC-EEEEEEEeCcEEEEE
Q 032095 2 ILAVLFANSEGNILVERFNGVPAEERLH-----WRSFLVK---LGADNLKGVKNEELLVASHKS-VYIVYTVLGDVSIFV 72 (147)
Q Consensus 2 I~~ili~n~~G~~~l~k~Y~~~~~~~~~-----~~~~~~~---i~~~~~~~~~~~~~~i~~~~~-~~ivy~~~~dl~~~~ 72 (147)
+++++|+|+.|..++.|-|..+..+... +..-++. +..+...-...+.-.++..++ ...+|+...++-|++
T Consensus 3 ve~~~iINksGglifqref~~~et~lnsneyLiLastlhgV~aI~tq~~p~~gssg~~~l~~~~f~m~I~qT~TG~kFV~ 82 (134)
T COG5122 3 VEQFFIINKSGGLIFQREFGEGETELNSNEYLILASTLHGVSAILTQTIPLPGSSGRLVLYFRNFVMTIFQTTTGTKFVF 82 (134)
T ss_pred eeEEEEEecCCcEEEEEeccCCccccCcccEEEEeechhhhhhhhhhcccCCCCCceEEEEeccEEEEEEEecCCcEEEE
Confidence 7899999999999999999652221100 1111111 111110000111112445555 566889999999999
Q ss_pred EEcC-CCCHHHHHHHHHHHHHHHHhHhcCC
Q 032095 73 VGKD-EYDELALAEVIFAITSAVKDACGKI 101 (147)
Q Consensus 73 v~~~-~eNel~l~e~l~~~~e~L~~~~~~~ 101 (147)
++.+ ..|.+.- ++.+++..++|.-+|
T Consensus 83 ~~~k~t~na~~q---l~kiY~lYsdYV~kn 109 (134)
T COG5122 83 VAEKRTVNALFQ---LQKIYSLYSDYVTKN 109 (134)
T ss_pred EecCCchhHHHH---HHHHHHHHHHHhhcC
Confidence 9954 4554433 677888888887554
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=84.29 E-value=8.5 Score=24.56 Aligned_cols=49 Identities=10% Similarity=0.164 Sum_probs=43.4
Q ss_pred eEEEecCEEEEEEEeCcEEEEEEEcCCCCHHHHHHHHHHHHHHHHhHhc
Q 032095 51 LVASHKSVYIVYTVLGDVSIFVVGKDEYDELALAEVIFAITSAVKDACG 99 (147)
Q Consensus 51 ~i~~~~~~~ivy~~~~dl~~~~v~~~~eNel~l~e~l~~~~e~L~~~~~ 99 (147)
.....+++.+-|..-+++.++++++.+...-..+.+|+.+.+-...-++
T Consensus 17 ~s~~~~~~~fh~~~~~~i~~~citd~~~~~r~aF~fL~~i~~~F~~~~~ 65 (83)
T PF13774_consen 17 MSYESGNYVFHYLVEDGIAYLCITDKSYPKRVAFAFLEEIKQEFIQTYG 65 (83)
T ss_dssp EEEEETTEEEEEEEETTEEEEEEEETTS-HHHHHHHHHHHHHHHHHHCT
T ss_pred EEEEECCEEEEEEEcCCeEEEEEEcCCCCcchHHHHHHHHHHHHHHHcC
Confidence 3566889999999999999999999999999999999999999888876
No 19
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=80.69 E-value=24 Score=27.33 Aligned_cols=100 Identities=15% Similarity=0.147 Sum_probs=65.6
Q ss_pred CceEEEEEe-CCCCEEEEecC--CCCHHHHHHHHHHHHHHhcccCCCCCCccceEEEecCEEEEEEEeCcEEEEEEEcCC
Q 032095 1 MILAVLFAN-SEGNILVERFN--GVPAEERLHWRSFLVKLGADNLKGVKNEELLVASHKSVYIVYTVLGDVSIFVVGKDE 77 (147)
Q Consensus 1 MI~~ili~n-~~G~~~l~k~Y--~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~ 77 (147)
||..-+|.- ++|-++.+-.= ..+...-...+.+.+.+.++- .+.+..+. -++.|.+.+-|...+++++.++++.+
T Consensus 1 mi~~T~I~RV~DGLPLa~s~d~~e~~~~s~~e~r~q~K~L~kkL-s~~s~~r~-Sietg~f~fHfli~~~Vcylvicd~~ 78 (216)
T KOG0862|consen 1 MILLTLIARVRDGLPLAASTDDNEQSGDSLLEYRQQAKSLFKKL-SQQSPTRC-SIETGPFVFHFLIESGVCYLVICDKS 78 (216)
T ss_pred CceeEEEEEecCCcccccccCcccCCCchHHHHHHHHHHHHHhc-cCCCCccc-ccccCCeEEEEEecCCEEEEEEecCC
Confidence 455444444 46666655432 112222235555666666432 11111111 23456799999999999999999999
Q ss_pred CCHHHHHHHHHHHHHHHHhHhcCCC
Q 032095 78 YDELALAEVIFAITSAVKDACGKIP 102 (147)
Q Consensus 78 eNel~l~e~l~~~~e~L~~~~~~~v 102 (147)
..--+.+..|+.+.+-+.+.++.++
T Consensus 79 yP~kLAF~YLedL~~EF~~~~~~~~ 103 (216)
T KOG0862|consen 79 YPRKLAFSYLEDLAQEFDKSYGKNI 103 (216)
T ss_pred CcHHHHHHHHHHHHHHHHHhccccc
Confidence 9999999999999999999887654
No 20
>KOG0997 consensus Uncharacterized conserved protein Sand [Function unknown]
Probab=75.27 E-value=54 Score=28.58 Aligned_cols=84 Identities=8% Similarity=0.080 Sum_probs=52.7
Q ss_pred EEEEEeCCCCEEEEecCCCC-----HHHHHHHHHHHHHHhcccCCCCCCccceEEEecCEEEEEEEeCcEEEEEEEcCCC
Q 032095 4 AVLFANSEGNILVERFNGVP-----AEERLHWRSFLVKLGADNLKGVKNEELLVASHKSVYIVYTVLGDVSIFVVGKDEY 78 (147)
Q Consensus 4 ~ili~n~~G~~~l~k~Y~~~-----~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~~e 78 (147)
-+||+.+.|++++++|=... .+-.+....|.+. + ++ ....+..+|+++|+-.-+-|+++++...+.
T Consensus 119 hifilseaGKPiyS~~gs~e~l~stmGv~~alISf~q~----~----~~-~i~si~a~g~k~vfl~kspl~LvA~s~t~~ 189 (523)
T KOG0997|consen 119 HIFILSEAGKPIYSRHGSDEALSSTMGVMQALISFFQV----S----GL-AITSIHAFGNKLVFLQKSPLLLVAVSRTSQ 189 (523)
T ss_pred eEEEEecCCCceeeecCcHHHHHHHHHHHHHHHHHHhh----C----Cc-eEEEEEecCceEEEEecCcEEEEEEccccc
Confidence 48999999999999997752 2223333333211 1 11 111345679999999999999999999755
Q ss_pred CHHH-HHHHHHHHHHHHHh
Q 032095 79 DELA-LAEVIFAITSAVKD 96 (147)
Q Consensus 79 Nel~-l~e~l~~~~e~L~~ 96 (147)
..-- +.++...+..+|+.
T Consensus 190 Sa~qL~~qL~~ly~QIlS~ 208 (523)
T KOG0997|consen 190 SAAQLLQQLLLLYCQILSI 208 (523)
T ss_pred CHHHHHHHHHHHHHHHHHH
Confidence 4333 33444444444443
No 21
>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=68.98 E-value=26 Score=22.07 Aligned_cols=69 Identities=16% Similarity=0.159 Sum_probs=36.6
Q ss_pred ceEEEEEeCCCCEEEEecCCCCHHHH-H----HHHHHHHHHhcccCCCCCCccceEEEecCEEEEEEEeCc-EEEEE
Q 032095 2 ILAVLFANSEGNILVERFNGVPAEER-L----HWRSFLVKLGADNLKGVKNEELLVASHKSVYIVYTVLGD-VSIFV 72 (147)
Q Consensus 2 I~~ili~n~~G~~~l~k~Y~~~~~~~-~----~~~~~~~~i~~~~~~~~~~~~~~i~~~~~~~ivy~~~~d-l~~~~ 72 (147)
+.+.+++|++|.++.+.-...+..++ . .+-..-.+.. +... ..+.+.-.+..++..++-.+.++ .++++
T Consensus 15 v~~~~l~~~dG~~i~~~~~~~~~~~~~aa~~a~~~~~~~~~~-~~l~-~~~~~~v~i~~~~~~i~i~~~~~~~~L~v 89 (91)
T PF03259_consen 15 VRGAVLVDKDGLVIASSGIDDDDAEKLAAMAASLLAAAEKLA-KELG-EGELEQVRIETEKGEIIITPVGDFYLLVV 89 (91)
T ss_dssp EEEEEEEETTSEEEEETSSSHHHHHHHHHHHHHHHHHHHHHH-HHHT-TSSEEEEEEEESSEEEEEEECSTCEEEEE
T ss_pred eeEEEEEcCCCCEEEEecCCcccHHHHHHHHHHHHHHHHHHH-HHhC-CCCcEEEEEEECCCEEEEEEcCCCEEEEE
Confidence 57899999999999992222211111 1 1111111122 1111 12333446677788888888888 54444
No 22
>COG3322 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]
Probab=60.92 E-value=8.2 Score=31.33 Aligned_cols=21 Identities=10% Similarity=0.317 Sum_probs=19.3
Q ss_pred ceEEEEEeCCCCEEEEecCCC
Q 032095 2 ILAVLFANSEGNILVERFNGV 22 (147)
Q Consensus 2 I~~ili~n~~G~~~l~k~Y~~ 22 (147)
+.++|++|.+|+++++|.+++
T Consensus 104 ~d~vf~vd~~G~~vy~~~~d~ 124 (295)
T COG3322 104 LDGVFVVDPSGKLVYSKLVDQ 124 (295)
T ss_pred ccEEEEECCCCCEEEEeeecc
Confidence 468999999999999999987
No 23
>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=49.52 E-value=19 Score=23.93 Aligned_cols=30 Identities=13% Similarity=0.036 Sum_probs=23.0
Q ss_pred CCHHHHHhc----HHHHHHHHHHHhhCCEEeeeC
Q 032095 102 PTERLFLDK----YGKICLCLDEIVWKGLLENTE 131 (147)
Q Consensus 102 v~e~~i~~n----~~~v~~lLDEiid~G~i~etd 131 (147)
+.-..|... -..|..++|++++.|+|..|-
T Consensus 66 v~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi 99 (102)
T PF08784_consen 66 VHVDEIAQQLGMSENEVRKALDFLSNEGHIYSTI 99 (102)
T ss_dssp EEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEESS
T ss_pred ccHHHHHHHhCcCHHHHHHHHHHHHhCCeEeccc
Confidence 444555444 478899999999999999873
No 24
>PF05228 CHASE4: CHASE4 domain; InterPro: IPR007892 CHASE4 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are upstream of signal transduction pathways in prokaryotes. Specifically, CHASE4 domains are found in histidine kinases in archaea and in predicted diguanylate cyclases/phosphodiesterases in bacteria. Environmental factors that are recognised by CHASE4 domains are not known at this time [].
Probab=48.62 E-value=62 Score=22.60 Aligned_cols=21 Identities=10% Similarity=0.275 Sum_probs=17.9
Q ss_pred ceEEEEEeCCCCEEE--EecCCC
Q 032095 2 ILAVLFANSEGNILV--ERFNGV 22 (147)
Q Consensus 2 I~~ili~n~~G~~~l--~k~Y~~ 22 (147)
+.+++++|.+|++++ ++.++.
T Consensus 50 ~d~~~~~d~~g~~~~~~~~~~~~ 72 (161)
T PF05228_consen 50 LDLIFILDPDGRVLYSSSKGYDF 72 (161)
T ss_pred ccEEEEEcCCCCEEEEeccCccc
Confidence 568999999999999 777765
No 25
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=47.63 E-value=18 Score=17.69 Aligned_cols=17 Identities=18% Similarity=0.403 Sum_probs=14.4
Q ss_pred cHHHHHHHHHHHhhCCE
Q 032095 110 KYGKICLCLDEIVWKGL 126 (147)
Q Consensus 110 n~~~v~~lLDEiid~G~ 126 (147)
+++.+..+++||.+.|+
T Consensus 15 ~~~~a~~~~~~M~~~g~ 31 (31)
T PF01535_consen 15 QFEEALEVFDEMRERGI 31 (31)
T ss_pred hHHHHHHHHHHHhHCcC
Confidence 67888899999998874
No 26
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=47.63 E-value=18 Score=18.15 Aligned_cols=17 Identities=18% Similarity=0.167 Sum_probs=14.4
Q ss_pred cHHHHHHHHHHHhhCCE
Q 032095 110 KYGKICLCLDEIVWKGL 126 (147)
Q Consensus 110 n~~~v~~lLDEiid~G~ 126 (147)
+++.+..++++|...|+
T Consensus 16 ~~~~a~~~~~~M~~~gv 32 (34)
T PF13812_consen 16 DPDAALQLFDEMKEQGV 32 (34)
T ss_pred CHHHHHHHHHHHHHhCC
Confidence 56778999999999884
No 27
>PF05184 SapB_1: Saposin-like type B, region 1; InterPro: IPR007856 Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].; GO: 0006629 lipid metabolic process; PDB: 1N69_C 1QDM_C 4DDJ_A 2DOB_A 1OF9_A 2Z9A_A 1M12_A 2GTG_A 1SN6_A 2QYP_B ....
Probab=44.63 E-value=24 Score=18.90 Aligned_cols=31 Identities=13% Similarity=0.179 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHhHhcCCCCHHHHHhcHHHHH
Q 032095 85 EVIFAITSAVKDACGKIPTERLFLDKYGKIC 115 (147)
Q Consensus 85 e~l~~~~e~L~~~~~~~v~e~~i~~n~~~v~ 115 (147)
++.+.++..++.+++++-++..|..-++.++
T Consensus 5 ~~C~~~v~~i~~~l~~~~t~~~I~~~l~~~C 35 (39)
T PF05184_consen 5 DICKFVVKEIEKLLKNNKTEEEIKKALEKAC 35 (39)
T ss_dssp HHHHHHHHHHHHHHHSTCHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHcCccHHHHHHHHHHHH
Confidence 5677888888898988888988887666654
No 28
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=42.52 E-value=1.5e+02 Score=22.48 Aligned_cols=48 Identities=13% Similarity=0.115 Sum_probs=37.0
Q ss_pred EEEecC-EEEEEEEeCcEEEEEEEcCCCCHHHHHHHHHHHHHHHHhHhcCC
Q 032095 52 VASHKS-VYIVYTVLGDVSIFVVGKDEYDELALAEVIFAITSAVKDACGKI 101 (147)
Q Consensus 52 i~~~~~-~~ivy~~~~dl~~~~v~~~~eNel~l~e~l~~~~e~L~~~~~~~ 101 (147)
+++.+. ...+|+...++-|+++++... -....+|+.+++.-++|--+|
T Consensus 125 ~LetdtF~l~~~QTlTG~KFVvis~~~~--~~aD~lLrKiYelYsDyvlKN 173 (199)
T KOG3369|consen 125 VLETDTFTLHIFQTLTGTKFVVIAEPGT--QGADSLLRKIYELYSDYVLKN 173 (199)
T ss_pred EEEeccEEEEEEEccCCcEEEEEecCCc--hhHHHHHHHHHHHHHHHhhcC
Confidence 444554 566889999999999999765 456778899999999887554
No 29
>KOG0861 consensus SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=40.97 E-value=1.6e+02 Score=22.35 Aligned_cols=88 Identities=14% Similarity=0.185 Sum_probs=50.1
Q ss_pred ceEEEEEeCCCC--EEEEecCCC---CHHHHH---HHHHHHHH-HhcccCCCCCCccceEEEecCE-EEEEEEeCcEEEE
Q 032095 2 ILAVLFANSEGN--ILVERFNGV---PAEERL---HWRSFLVK-LGADNLKGVKNEELLVASHKSV-YIVYTVLGDVSIF 71 (147)
Q Consensus 2 I~~ili~n~~G~--~~l~k~Y~~---~~~~~~---~~~~~~~~-i~~~~~~~~~~~~~~i~~~~~~-~ivy~~~~dl~~~ 71 (147)
|.++.+++..+. +++++-++- +.-+|. .+-.|..+ +.++. .+..+..+ .++.| .-+|-|..+|+-+
T Consensus 3 i~sl~V~~~~~~~~~ll~~a~dls~FsfFqRssV~Efm~F~sktvaeRt---~~g~rqsv-k~~~Y~~h~yvrndgL~~V 78 (198)
T KOG0861|consen 3 IYSLSVLHKGTSDVKLLKTASDLSSFSFFQRSSVQEFMTFISKTVAERT---GPGQRQSV-KHEEYLVHVYVRNDGLCGV 78 (198)
T ss_pred eEEEEEEeeCCcchhhhhhhcccccccceeeccHHHHHHHHHHHHHHhc---Cccccccc-ccceeEEEEEEecCCeeEE
Confidence 667888887443 344444442 111232 34444444 33222 22222222 23444 4467777799999
Q ss_pred EEEcCCCCHHHHHHHHHHHHHH
Q 032095 72 VVGKDEYDELALAEVIFAITSA 93 (147)
Q Consensus 72 ~v~~~~eNel~l~e~l~~~~e~ 93 (147)
++++.++.--..+.+|+.+.+-
T Consensus 79 ~~~D~eYP~rvA~tLL~kvld~ 100 (198)
T KOG0861|consen 79 LIADDEYPVRVAFTLLNKVLDE 100 (198)
T ss_pred EEecCcCchhHHHHHHHHHHHH
Confidence 9999999988888877765443
No 30
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=35.83 E-value=33 Score=21.38 Aligned_cols=24 Identities=25% Similarity=0.457 Sum_probs=18.0
Q ss_pred CCEEeeeCHH--HHHHHHhcCCCCCC
Q 032095 124 KGLLENTEKD--RIRRLVRLKPPNEF 147 (147)
Q Consensus 124 ~G~i~etd~~--~i~~~i~~~~~~~~ 147 (147)
.|++.-+||+ .|++|+..+-|.+|
T Consensus 34 ~G~~iIidpe~SeIAkrlgi~~Pg~y 59 (64)
T COG2093 34 FGLLIIIDPEKSEIAKRLGIKIPGKY 59 (64)
T ss_pred ccEEEEEcCcHHHHHHHhCCCCCceE
Confidence 4766555554 59999999999875
No 31
>PF14903 WG_beta_rep: WG containing repeat
Probab=32.62 E-value=52 Score=16.77 Aligned_cols=16 Identities=13% Similarity=0.333 Sum_probs=13.2
Q ss_pred EEeCCCCEEEEecCCC
Q 032095 7 FANSEGNILVERFNGV 22 (147)
Q Consensus 7 i~n~~G~~~l~k~Y~~ 22 (147)
++|.+|+.++.--|+.
T Consensus 3 ~id~~G~~vi~~~yd~ 18 (35)
T PF14903_consen 3 YIDKNGKIVIPPKYDE 18 (35)
T ss_pred EEeCCCCEEEEccccC
Confidence 5789999998887776
No 32
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=31.23 E-value=41 Score=16.45 Aligned_cols=18 Identities=11% Similarity=0.202 Sum_probs=15.1
Q ss_pred cHHHHHHHHHHHhhCCEE
Q 032095 110 KYGKICLCLDEIVWKGLL 127 (147)
Q Consensus 110 n~~~v~~lLDEiid~G~i 127 (147)
+++.+..++++|...|+.
T Consensus 15 ~~~~a~~~~~~M~~~g~~ 32 (35)
T TIGR00756 15 RVEEALELFKEMLERGIE 32 (35)
T ss_pred CHHHHHHHHHHHHHcCCC
Confidence 567888999999998864
No 33
>PF13041 PPR_2: PPR repeat family
Probab=28.86 E-value=55 Score=18.29 Aligned_cols=19 Identities=16% Similarity=0.277 Sum_probs=16.6
Q ss_pred cHHHHHHHHHHHhhCCEEe
Q 032095 110 KYGKICLCLDEIVWKGLLE 128 (147)
Q Consensus 110 n~~~v~~lLDEiid~G~i~ 128 (147)
+++.+..+++||...|+.-
T Consensus 18 ~~~~a~~l~~~M~~~g~~P 36 (50)
T PF13041_consen 18 KFEEALKLFKEMKKRGIKP 36 (50)
T ss_pred CHHHHHHHHHHHHHcCCCC
Confidence 7889999999999999753
No 34
>KOG0903 consensus Phosphatidylinositol 4-kinase, involved in intracellular trafficking and secretion [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=27.77 E-value=3.6e+02 Score=25.15 Aligned_cols=92 Identities=15% Similarity=0.112 Sum_probs=55.5
Q ss_pred HHHHHHHHHHHhccc-------CCCCCCccceEEEecCEEEEEEEeCcEEEEEEEcC-CC-CHHHHHHHHHHHHHHHH--
Q 032095 27 RLHWRSFLVKLGADN-------LKGVKNEELLVASHKSVYIVYTVLGDVSIFVVGKD-EY-DELALAEVIFAITSAVK-- 95 (147)
Q Consensus 27 ~~~~~~~~~~i~~~~-------~~~~~~~~~~i~~~~~~~ivy~~~~dl~~~~v~~~-~e-Nel~l~e~l~~~~e~L~-- 95 (147)
+++++.|++.+..-. +|.. .+..|+.-+.-.|+|.-++ |++-+++ +. =|-+=+-+-.-+.|+|+
T Consensus 677 k~AQrNFvqSlagYSLvcYlLQvKDR--HNGNILiD~EGHIIHIDFG---FmLsnsPgnvgFEsAPFKLT~EylEvmgG~ 751 (847)
T KOG0903|consen 677 KSAQRNFVQSLAGYSLVCYLLQVKDR--HNGNILIDEEGHIIHIDFG---FMLSNSPGNVGFESAPFKLTTEYLEVMGGL 751 (847)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhcccc--cCCceEecCCCCEEEEeee---eEecCCCCCcccccCchhhHHHHHHHhcCC
Confidence 678888887654311 1221 2233776666778888777 7777665 43 35555555555555555
Q ss_pred -----hHhcCCCCHH---HHHhcHHHHHHHHHHHhhCC
Q 032095 96 -----DACGKIPTER---LFLDKYGKICLCLDEIVWKG 125 (147)
Q Consensus 96 -----~~~~~~v~e~---~i~~n~~~v~~lLDEiid~G 125 (147)
+||+ .++.. .++.|.+++.++. ||+++|
T Consensus 752 ~~d~FdyfK-~L~l~gf~a~RKhadrIv~lv-EiMq~~ 787 (847)
T KOG0903|consen 752 DSDMFDYFK-SLMLQGFMALRKHADRIVLLV-EIMQDG 787 (847)
T ss_pred cHHHHHHHH-HHHHHHHHHHHHHHHHHHHHH-HHhhcc
Confidence 3343 23333 5788999999988 777664
No 35
>PF06694 Plant_NMP1: Plant nuclear matrix protein 1 (NMP1); InterPro: IPR010604 This family consists of several plant specific nuclear matrix protein 1 (NMP1) sequences. Nuclear Matrix Protein 1 is a ubiquitously expressed 36 kDa protein, which has no homologues in animals and fungi, but is highly conserved among flowering and non-flowering plants. NMP1 is located both in the cytoplasm and nucleus and that the nuclear fraction is associated with the nuclear matrix. NMP1 is a candidate for a plant-specific structural protein with a function both in the nucleus and cytoplasm [].
Probab=26.28 E-value=1.6e+02 Score=24.16 Aligned_cols=40 Identities=20% Similarity=0.132 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHhHhcCCCCHHHHHhcHHHHHHHHHHHh
Q 032095 83 LAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIV 122 (147)
Q Consensus 83 l~e~l~~~~e~L~~~~~~~v~e~~i~~n~~~v~~lLDEii 122 (147)
-.++|+.+++.+..-..-+=.+-.+.+++.+-+.++|-+.
T Consensus 102 ~~~~l~~IVDlVeas~~~~n~e~Sl~eQ~~kD~~LiD~Ia 141 (325)
T PF06694_consen 102 RAEFLRLIVDLVEASMYADNPEWSLDEQFAKDIQLIDAIA 141 (325)
T ss_pred HHHHHHHHHHHHHHHHhhcCchhhHHHHHHHHHHHHHHHH
Confidence 3677888888888776543367789999999999999988
No 36
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=25.34 E-value=36 Score=20.10 Aligned_cols=15 Identities=27% Similarity=0.483 Sum_probs=11.3
Q ss_pred HHHHHHHHhhCCEEe
Q 032095 114 ICLCLDEIVWKGLLE 128 (147)
Q Consensus 114 v~~lLDEiid~G~i~ 128 (147)
.-..|||+|..|.|.
T Consensus 15 L~dtLDeli~~~~I~ 29 (49)
T PF02268_consen 15 LTDTLDELIQEGKIT 29 (49)
T ss_dssp HHHHHHHHHHTTSS-
T ss_pred HHHHHHHHHHcCCCC
Confidence 346799999999763
No 37
>cd03671 Ap4A_hydrolase_plant_like Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant enzymes fall into one group (represented by this subfamily) and fungi/animals/archaea enzymes fall into another. Bacterial enzymes are found in both subfamilies. Ap4A is a potential by-product of aminoacyl tRNA synthesis, and accumulation of Ap4A has been implicated in a range of biological events, such as DNA replication, cellular differentiation, heat shock, metabolic stress, and apoptosis. Ap4A hydrolase cleaves Ap4A asymmetrically into ATP and AMP. It is important in the invasive properties of bacteria and thus presents a potential target for the inhibition of such invasive bacteria. Besides the signature nudix motif (G[X5]E[X7]REUXEEXGU where U is Ile, Leu, or Val), Ap4A hydrolase is structurally
Probab=24.17 E-value=88 Score=21.82 Aligned_cols=19 Identities=26% Similarity=0.457 Sum_probs=15.7
Q ss_pred EEEEEeCCCCEEEEecCCC
Q 032095 4 AVLFANSEGNILVERFNGV 22 (147)
Q Consensus 4 ~ili~n~~G~~~l~k~Y~~ 22 (147)
+++|+|.+|++++.|.+..
T Consensus 7 ~~ii~~~~~~vLL~~r~~~ 25 (147)
T cd03671 7 GVVLFNEDGKVFVGRRIDT 25 (147)
T ss_pred EEEEEeCCCEEEEEEEcCC
Confidence 6788899999999887763
No 38
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=23.44 E-value=1.8e+02 Score=21.19 Aligned_cols=50 Identities=12% Similarity=-0.020 Sum_probs=29.6
Q ss_pred HHHHHHhHhcCCCCHHHHHhcHHHHHHHHHHHhhCCEEeee------CHHHHHHHHh
Q 032095 90 ITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENT------EKDRIRRLVR 140 (147)
Q Consensus 90 ~~e~L~~~~~~~v~e~~i~~n~~~v~~lLDEiid~G~i~et------d~~~i~~~i~ 140 (147)
+.+.|+++++ .+.+++.-+..+.--+.+||-..+|.-.|- +|+.+++.+.
T Consensus 6 fL~~L~~~L~-~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG~P~~iA~~i~ 61 (181)
T PF08006_consen 6 FLNELEKYLK-KLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIAREIL 61 (181)
T ss_pred HHHHHHHHHH-cCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHHHH
Confidence 4556666665 377777776666666666666666632221 5555555543
No 39
>COG3657 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.41 E-value=1e+02 Score=20.88 Aligned_cols=64 Identities=13% Similarity=0.057 Sum_probs=32.7
Q ss_pred CEEEEecCCC--CHHHHHHHHHHHHHHhcccCCCCCCccce-----EEEecCEEEEEEEeCcEEEEEEEcC
Q 032095 13 NILVERFNGV--PAEERLHWRSFLVKLGADNLKGVKNEELL-----VASHKSVYIVYTVLGDVSIFVVGKD 76 (147)
Q Consensus 13 ~~~l~k~Y~~--~~~~~~~~~~~~~~i~~~~~~~~~~~~~~-----i~~~~~~~ivy~~~~dl~~~~v~~~ 76 (147)
.-.+++|.+. +...++.+.+.+..+...|....+.+... |-.-.|+.+-|.+.+++.+++++-.
T Consensus 9 ~d~F~~W~~kLkD~~Aka~I~~Rl~rl~~GN~GD~kpvgeGV~ELRId~GpGyRvY~~~~g~v~i~lLCgG 79 (100)
T COG3657 9 TDTFSEWLKKLKDRRAKAKIAARLDRLALGNFGDVKPVGEGVSELRIDHGPGYRVYFQQRGLVLILLLCGG 79 (100)
T ss_pred hHHHHHHHHHHHhHHHHHHHHHHHHHHhcCCCcCccccccchhhheeccCCceEEEEEecCcEEEEEeccC
Confidence 3334445443 22334555555555543332111112111 2223479999999999877766553
No 40
>PF13998 MgrB: MgrB protein
Probab=22.89 E-value=61 Score=17.00 Aligned_cols=16 Identities=25% Similarity=0.090 Sum_probs=11.9
Q ss_pred HHHHHHHhhCCEEeee
Q 032095 115 CLCLDEIVWKGLLENT 130 (147)
Q Consensus 115 ~~lLDEiid~G~i~et 130 (147)
.+.||-++|.|.....
T Consensus 3 llald~~CDQg~~F~~ 18 (29)
T PF13998_consen 3 LLALDSYCDQGEQFFS 18 (29)
T ss_pred HHHHHHHhcCCCCcee
Confidence 3679999999965443
No 41
>cd03016 PRX_1cys Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by reducing and detoxifying hydrogen peroxide, peroxynitrite, and organic hydroperoxides. As with all other PRXs, a cysteine sulfenic acid intermediate is formed upon reaction of 1-cys PRX with its substrates. Having no resolving cysteine, the oxidized enzyme is resolved by an external small-molecule or protein reductant such as thioredoxin or glutaredoxin. Similar to typical 2-cys PRX, 1-cys PRX forms a functional dimeric unit with a B-type interface, as well as a decameric structure which is stabilized in the reduced form of the enzyme. Other oligomeric forms, tetramers and hexamers, have also been reported. Mammalian 1-cys PRX is localized cellularly in the cytosol and is expressed at high levels in brain, eye, testes an
Probab=22.13 E-value=1.5e+02 Score=22.10 Aligned_cols=19 Identities=16% Similarity=0.246 Sum_probs=16.7
Q ss_pred EEEEEeCCCCEEEEecCCC
Q 032095 4 AVLFANSEGNILVERFNGV 22 (147)
Q Consensus 4 ~ili~n~~G~~~l~k~Y~~ 22 (147)
+.+|+|.+|+++....|..
T Consensus 119 ~~fiID~~G~I~~~~~~~~ 137 (203)
T cd03016 119 AVFIIDPDKKIRLILYYPA 137 (203)
T ss_pred EEEEECCCCeEEEEEecCC
Confidence 6899999999999988864
No 42
>cd04685 Nudix_Hydrolase_26 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily requires a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=21.64 E-value=1e+02 Score=21.40 Aligned_cols=18 Identities=17% Similarity=0.353 Sum_probs=15.2
Q ss_pred EEEEEeCCCCEEEEecCC
Q 032095 4 AVLFANSEGNILVERFNG 21 (147)
Q Consensus 4 ~ili~n~~G~~~l~k~Y~ 21 (147)
.++++|.+|++++.|..+
T Consensus 4 ~~~i~~~~g~vLl~r~~~ 21 (133)
T cd04685 4 RVVLLDPDDRVLLLRGDD 21 (133)
T ss_pred EEEEEcCCCeEEEEEEeC
Confidence 578999999999988754
No 43
>smart00836 DALR_1 DALR anticodon binding domain. This all alpha helical domain is the anticodon binding domain of Arginyl tRNA synthetase. This domain is known as the DALR domain after characteristic conserved amino acids PUBMED:10447505.
Probab=21.61 E-value=2.6e+02 Score=18.60 Aligned_cols=63 Identities=13% Similarity=0.085 Sum_probs=47.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHhHhcCCCCHHHHHhcHHHHHHHHHHHhhCCEEeeeC-HHHHHHHH
Q 032095 76 DEYDELALAEVIFAITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLLENTE-KDRIRRLV 139 (147)
Q Consensus 76 ~~eNel~l~e~l~~~~e~L~~~~~~~v~e~~i~~n~~~v~~lLDEiid~G~i~etd-~~~i~~~i 139 (147)
.++.|..++..+..+.+++...+.. .+-..+..-...+...++..-+.-.|+..+ .+.-..|+
T Consensus 34 ~~~~E~~L~~~i~~~~~~i~~~~~~-~~~~~l~~~l~~L~~~~~~fy~~v~V~~~~~~~~~~~RL 97 (122)
T smart00836 34 TEPEELALLRLLARFPEVLEAAAET-LEPHRLANYLYDLASAFHSFYNKCRVLGEENPELRAARL 97 (122)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHH-CCcHHHHHHHHHHHHHHHHHHccCcccCCCCHHHHHHHH
Confidence 3678888999999999988877753 455667778888889999999888777766 55444444
No 44
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.86 E-value=3.3e+02 Score=19.61 Aligned_cols=83 Identities=14% Similarity=0.075 Sum_probs=50.5
Q ss_pred ceEEEEEeCCCCEEEEecCCCC---HHHHH-----------HHHHHHHHHhcccCCCCCCccceEEEe--cCEEEEEEE-
Q 032095 2 ILAVLFANSEGNILVERFNGVP---AEERL-----------HWRSFLVKLGADNLKGVKNEELLVASH--KSVYIVYTV- 64 (147)
Q Consensus 2 I~~ili~n~~G~~~l~k~Y~~~---~~~~~-----------~~~~~~~~i~~~~~~~~~~~~~~i~~~--~~~~ivy~~- 64 (147)
|.++.|+|++|.-++.+-|..+ ..++. .++.+..++.. .+....+..+ +.+++-|-.
T Consensus 3 iy~~yIFdR~g~Cl~y~EW~r~~~s~~~~eee~KL~yGmlFSlkS~v~Kls~------~d~k~~f~sy~Ts~YklhfyeT 76 (140)
T KOG3368|consen 3 IYNFYIFDRNGVCLFYREWNRTKQSGIPNEEEAKLMYGMLFSLKSFVSKLSP------GDVKDGFLSYKTSKYKLHFYET 76 (140)
T ss_pred EEEEEEEcCCccEEEehhcccccccCCchhHHHHHHHHHHhhHHHHHHhcCC------CCcccCeeEEeeceeEEEEEEc
Confidence 7889999999999988877651 11111 23333333331 1222224433 346665544
Q ss_pred eCcEEEEEEEcCCCCHHHHHHHHHHHHH
Q 032095 65 LGDVSIFVVGKDEYDELALAEVIFAITS 92 (147)
Q Consensus 65 ~~dl~~~~v~~~~eNel~l~e~l~~~~e 92 (147)
-.+|.|++.++..... +-++||.++.
T Consensus 77 ptglk~vl~Tdpk~~~--ir~vLq~IYs 102 (140)
T KOG3368|consen 77 PTGLKFVLNTDPKAGS--IRDVLQYIYS 102 (140)
T ss_pred CCCcEEEEecCCCccc--HHHHHHHHHH
Confidence 4689999999886654 5678888877
No 45
>PF02334 RTP: Replication terminator protein; InterPro: IPR003432 The bacterial replication terminator protein (RTP) plays a role in the termination of DNA replication by impeding replication fork movement. Two RTP dimers bind to the two inverted repeat regions at the termination site.; GO: 0003677 DNA binding, 0006274 DNA replication termination; PDB: 2DPU_A 2DPD_A 1F4K_A 1J0R_B 2EFW_F 2DQR_B 1BM9_B.
Probab=20.72 E-value=94 Score=21.74 Aligned_cols=34 Identities=15% Similarity=0.269 Sum_probs=22.2
Q ss_pred HHHHHHhHhcCCCCHHHHHhcHHHHHHHHHHHhhCCEE
Q 032095 90 ITSAVKDACGKIPTERLFLDKYGKICLCLDEIVWKGLL 127 (147)
Q Consensus 90 ~~e~L~~~~~~~v~e~~i~~n~~~v~~lLDEiid~G~i 127 (147)
+.+.|..=|+. +. -.=|-..+|-.|+|++++|++
T Consensus 37 ~Ld~lr~EFk~-~G---y~P~hsEvYraLHeL~~dGil 70 (122)
T PF02334_consen 37 LLDELRSEFKP-LG---YRPNHSEVYRALHELVDDGIL 70 (122)
T ss_dssp HHHHHHHHHTT-TT-------HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHhhh-cC---CCCCHHHHHHHHHHHHhhhHH
Confidence 34555555642 33 444677899999999999998
No 46
>cd04670 Nudix_Hydrolase_12 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=20.30 E-value=1.3e+02 Score=20.14 Aligned_cols=18 Identities=22% Similarity=0.252 Sum_probs=14.5
Q ss_pred EEEEEeCCCCEEEEecCC
Q 032095 4 AVLFANSEGNILVERFNG 21 (147)
Q Consensus 4 ~ili~n~~G~~~l~k~Y~ 21 (147)
+.+++|.+|++++.|.+.
T Consensus 6 ~~~v~~~~~~vLl~~r~~ 23 (127)
T cd04670 6 GGLVLNEKNEVLVVQERN 23 (127)
T ss_pred EEEEEcCCCeEEEEEccC
Confidence 467889999999987665
Done!