Query 031317
Match_columns 161
No_of_seqs 104 out of 734
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 12:24:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031317.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031317hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5030 APS2 Clathrin adaptor 100.0 2.1E-42 4.6E-47 258.8 15.0 144 1-144 1-144 (152)
2 PF01217 Clat_adaptor_s: Clath 100.0 7.8E-42 1.7E-46 258.2 18.3 141 1-141 1-141 (141)
3 KOG0934 Clathrin adaptor compl 100.0 1.3E-39 2.9E-44 243.2 8.6 142 1-142 1-142 (145)
4 KOG0936 Clathrin adaptor compl 100.0 4.2E-38 9.1E-43 239.2 14.8 146 1-146 1-152 (182)
5 KOG0935 Clathrin adaptor compl 100.0 4.3E-38 9.4E-43 230.9 12.1 141 1-141 1-142 (143)
6 KOG0938 Adaptor complexes medi 100.0 5.2E-31 1.1E-35 222.2 12.9 134 1-138 1-135 (446)
7 KOG3343 Vesicle coat complex C 100.0 1.5E-28 3.2E-33 188.0 12.5 135 2-139 9-147 (175)
8 KOG0937 Adaptor complexes medi 99.9 3E-23 6.6E-28 179.8 14.5 134 2-138 1-136 (424)
9 KOG2740 Clathrin-associated pr 99.9 1.4E-23 3E-28 178.3 9.6 140 1-142 1-142 (418)
10 COG5541 RET3 Vesicle coat comp 99.8 4.1E-20 8.8E-25 141.5 9.8 133 2-137 8-152 (187)
11 KOG2635 Medium subunit of clat 98.3 1.3E-05 2.8E-10 70.7 12.4 131 2-136 3-135 (512)
12 PF15001 AP-5_subunit_s1: AP-5 97.4 0.014 3.1E-07 46.6 15.0 77 54-130 103-180 (189)
13 PF03164 Mon1: Trafficking pro 96.2 0.18 3.8E-06 44.7 13.5 90 3-95 12-103 (415)
14 PF08923 MAPKK1_Int: Mitogen-a 95.4 0.32 6.8E-06 36.0 10.1 92 2-93 17-114 (119)
15 PF04099 Sybindin: Sybindin-li 95.2 0.35 7.5E-06 36.6 10.0 95 2-97 1-118 (142)
16 PF13774 Longin: Regulated-SNA 93.2 0.91 2E-05 30.7 7.8 48 49-96 18-65 (83)
17 KOG0859 Synaptobrevin/VAMP-lik 91.9 3.8 8.1E-05 33.2 10.8 89 5-97 4-93 (217)
18 KOG0862 Synaptobrevin/VAMP-lik 89.9 4.3 9.4E-05 33.1 9.5 74 26-100 31-104 (216)
19 COG5122 TRS23 Transport protei 85.2 6.6 0.00014 29.2 7.3 91 2-95 3-106 (134)
20 KOG0781 Signal recognition par 83.2 24 0.00052 32.5 11.4 113 1-117 1-117 (587)
21 KOG0997 Uncharacterized conser 82.9 18 0.0004 33.0 10.5 72 4-80 119-194 (523)
22 PF08006 DUF1700: Protein of u 80.2 5.5 0.00012 30.8 5.7 58 87-144 6-69 (181)
23 KOG3369 Transport protein part 66.8 65 0.0014 25.8 10.1 45 49-95 125-170 (199)
24 KOG0861 SNARE protein YKT6, sy 60.8 86 0.0019 25.1 10.6 89 2-91 3-101 (198)
25 PF04086 SRP-alpha_N: Signal r 60.2 92 0.002 25.6 9.0 50 49-98 21-72 (279)
26 COG3322 Predicted periplasmic 49.1 16 0.00035 31.2 2.8 22 2-23 104-125 (295)
27 PF05228 CHASE4: CHASE4 domain 41.2 94 0.002 22.6 5.6 21 2-22 50-72 (161)
28 PF01535 PPR: PPR repeat; Int 40.4 26 0.00057 17.9 1.9 18 105-122 14-31 (31)
29 PF09201 SRX: SRX; InterPro: 40.1 1.7E+02 0.0037 22.5 8.5 70 1-73 1-86 (148)
30 PF13812 PPR_3: Pentatricopept 35.8 33 0.00071 18.1 1.8 17 106-122 16-32 (34)
31 cd05165 PI3Kc_I Phosphoinositi 35.2 76 0.0016 27.9 4.8 90 46-136 221-325 (366)
32 PF09639 YjcQ: YjcQ protein; 34.2 75 0.0016 21.8 3.8 39 86-124 3-41 (88)
33 cd08324 CARD_NOD1_CARD4 Caspas 32.9 40 0.00086 23.6 2.2 44 100-143 7-50 (85)
34 TIGR00756 PPR pentatricopeptid 32.2 42 0.00092 17.3 1.9 19 106-124 15-33 (35)
35 PRK13190 putative peroxiredoxi 31.3 1E+02 0.0022 24.2 4.6 21 2-22 117-137 (202)
36 PF04614 Pex19: Pex19 protein 29.9 1.2E+02 0.0025 25.1 4.9 21 104-124 195-215 (248)
37 cd00896 PI3Kc_III Phosphoinosi 29.4 1.1E+02 0.0023 26.7 4.8 89 46-138 211-310 (350)
38 PF08784 RPA_C: Replication pr 28.3 58 0.0013 22.5 2.5 23 105-127 77-99 (102)
39 cd03016 PRX_1cys Peroxiredoxin 28.1 1.4E+02 0.003 23.4 4.9 20 3-22 118-137 (203)
40 COG4114 FhuF Uncharacterized F 27.8 1.7E+02 0.0036 24.4 5.3 40 78-118 147-187 (251)
41 PF03259 Robl_LC7: Roadblock/L 27.7 1.8E+02 0.0038 18.9 6.9 68 2-69 15-88 (91)
42 PF13041 PPR_2: PPR repeat fam 26.7 50 0.0011 19.4 1.7 22 105-126 17-38 (50)
43 PF14903 WG_beta_rep: WG conta 26.6 66 0.0014 17.3 2.1 17 7-23 3-19 (35)
44 cd05168 PI4Kc_III_beta Phospho 26.5 1.2E+02 0.0026 25.7 4.5 80 46-126 150-240 (293)
45 PF02268 TFIIA_gamma_N: Transc 26.1 1.3E+02 0.0027 18.9 3.4 29 110-141 15-43 (49)
46 smart00571 DDT domain in diffe 25.6 59 0.0013 21.0 2.0 17 76-92 6-22 (63)
47 PF08542 Rep_fac_C: Replicatio 23.8 1.4E+02 0.0031 19.7 3.7 31 106-136 19-49 (89)
48 COG0450 AhpC Peroxiredoxin [Po 23.4 1.9E+02 0.0041 23.3 4.8 21 2-22 124-144 (194)
49 cd00893 PI4Kc_III Phosphoinosi 23.0 1.2E+02 0.0026 25.7 3.8 80 46-126 148-238 (289)
50 PRK13191 putative peroxiredoxi 22.9 1.8E+02 0.0039 23.2 4.7 21 2-22 124-144 (215)
51 PF02791 DDT: DDT domain; Int 22.8 79 0.0017 20.1 2.1 18 76-93 6-23 (61)
52 PF11662 DUF3263: Protein of u 22.0 1.1E+02 0.0023 21.0 2.7 41 96-137 21-65 (77)
53 KOG1766 Enhancer of rudimentar 22.0 1.6E+02 0.0035 21.2 3.7 42 80-121 25-68 (104)
54 PF02334 RTP: Replication term 21.5 1.6E+02 0.0034 21.9 3.7 34 87-123 37-70 (122)
55 cd03671 Ap4A_hydrolase_plant_l 20.8 1E+02 0.0022 22.5 2.7 19 4-22 7-25 (147)
56 PRK15000 peroxidase; Provision 20.8 2.1E+02 0.0046 22.4 4.7 21 2-22 125-145 (200)
57 PRK13599 putative peroxiredoxi 20.5 2E+02 0.0044 22.9 4.5 21 2-22 119-139 (215)
58 cd00894 PI3Kc_IB_gamma Phospho 20.2 2E+02 0.0043 25.3 4.7 82 46-129 221-318 (365)
No 1
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=100.00 E-value=2.1e-42 Score=258.83 Aligned_cols=144 Identities=54% Similarity=0.935 Sum_probs=139.3
Q ss_pred CeEEEEEEcCCCCeEEEecCCCCCHHHHHHHHHHHHHHHhccCCCccceEEeCCeEEEEEEeCcEEEEEEecCCCCHHHH
Q 031317 1 MIHFVLLISRQGKVRLTKWYSPYTQKERSKVIRELSGVILTRGPKLCNFVEWRGYKVVYKRYASLYFCMCVDQEDNELEI 80 (161)
Q Consensus 1 MI~al~Iln~~G~~~l~K~Y~~~~~~~~~~~~~~i~~~i~~r~~~~~~i~~~~~~~~vy~~~~~L~f~~v~~~neNel~i 80 (161)
||++++|+|++|++||.|||.+.+.++|+++.+++++.+++|+.++|++++..+.++|||||++|||++++++++|||++
T Consensus 1 ~i~~vli~nrqgk~RL~K~yt~~~~~e~~kli~~i~~lIs~R~~ke~N~~e~k~~kiVYrrYA~LyF~f~Vd~~dnEl~i 80 (152)
T COG5030 1 MIKFVLIFNRQGKPRLVKWYTPVSDPEQAKLIADIYELISARKPKESNFIEGKNEKIVYRRYATLYFVFGVDNDDNELII 80 (152)
T ss_pred CeEEEEEEcCCCceeeeEeeccCCcHHHHHHHHHHHHHHHcCCchhcccccccCcEEEeeecCcEEEEEEEcCCCCcchH
Confidence 89999999999999999999999988999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcccchhhHHhhHHHHHHHHHHHHhCcEeeecCHHHHHHHHHhhhhhHHh
Q 031317 81 LEIIHHYVEILDRYFGSVCELDLIFNFHKAYYILDEILIAGELQESSKKTVARLIAAQDSLVET 144 (161)
Q Consensus 81 ~efL~~~ve~L~~yfg~v~E~~i~~Nf~~vy~lLDEmid~G~~~eT~~~~i~~~i~~~~~~~~~ 144 (161)
+++||.||++||+|||+|||+|+++||.++|.+||||+.+|.++||++..+++++...++.+..
T Consensus 81 L~lIh~FVE~lDr~FgnVCELdlIFNF~kv~~ILdE~i~gG~i~Es~~~~vl~~v~~lda~~~~ 144 (152)
T COG5030 81 LELIHNFVEILDRFFGNVCELDLIFNFQKVYAILDEMILGGEIIESSKNEVLEHVYALDAESTD 144 (152)
T ss_pred HHHHHHHHHHHHHHhccceeeEeEeeHHHHHHHHHHHHhCCeeeecCHHHHHHHHHHHHhhccc
Confidence 9999999999999999999999999999999999999999999999999999999988766543
No 2
>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=7.8e-42 Score=258.17 Aligned_cols=141 Identities=38% Similarity=0.673 Sum_probs=131.7
Q ss_pred CeEEEEEEcCCCCeEEEecCCCCCHHHHHHHHHHHHHHHhccCCCccceEEeCCeEEEEEEeCcEEEEEEecCCCCHHHH
Q 031317 1 MIHFVLLISRQGKVRLTKWYSPYTQKERSKVIRELSGVILTRGPKLCNFVEWRGYKVVYKRYASLYFCMCVDQEDNELEI 80 (161)
Q Consensus 1 MI~al~Iln~~G~~~l~K~Y~~~~~~~~~~~~~~i~~~i~~r~~~~~~i~~~~~~~~vy~~~~~L~f~~v~~~neNel~i 80 (161)
||+|++|+|++|+++++|||++.+.++++++.+++.+.+.++++..||++.+++++++|+++++|||+++++.++||+++
T Consensus 1 MI~~i~i~n~~G~~i~~k~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~dl~~~~v~~~~eNel~~ 80 (141)
T PF01217_consen 1 MIKAILILNSQGKRILSKYYRDVSEEERQKLFEKFIKKKSSRNSKQSPIFEHDNYRIVYKRYSDLYFVVVGDENENELLL 80 (141)
T ss_dssp SEEEEEEEETTSEEEEEEESSTSTSHHHHHHHHHHHHHHHTSSSSSTSEEEETTEEEEEEEETTEEEEEEESSTSBHHHH
T ss_pred CEEEEEEEcCCCCEEEehhcCCccHHHHHHHHHHHHHHHHhcccccceeeecccceeeeEeeccEEEEEEeecccchHHH
Confidence 99999999999999999999988877888889998888888877789999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcccchhhHHhhHHHHHHHHHHHHhCcEeeecCHHHHHHHHHhhhhh
Q 031317 81 LEIIHHYVEILDRYFGSVCELDLIFNFHKAYYILDEILIAGELQESSKKTVARLIAAQDSL 141 (161)
Q Consensus 81 ~efL~~~ve~L~~yfg~v~E~~i~~Nf~~vy~lLDEmid~G~~~eT~~~~i~~~i~~~~~~ 141 (161)
+++||+++++|+.|||++||.++++||++||++||||+|+|+|+|||++.|++++.+++++
T Consensus 81 ~e~l~~~v~~l~~~~~~v~e~~i~~N~~~v~~~LDEiid~G~i~etd~~~I~~~v~~~~~~ 141 (141)
T PF01217_consen 81 LEFLHRLVEVLDDYFGNVSEKDILENFDLVYLILDEIIDGGIILETDPNVILKRVTMQDSA 141 (141)
T ss_dssp HHHHHHHHHHHHHHHSS-SHHHHHHTHHHHHHHHHHHEETTEES--THHHHHHHHHHCCC-
T ss_pred HHHHHHhhhhhhhhhccccHHHHHHCHHHHHHHHHHHHhCCEEEECCHHHHHHHHHHhhcC
Confidence 9999999999999999999999999999999999999999999999999999999998763
No 3
>KOG0934 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.3e-39 Score=243.22 Aligned_cols=142 Identities=61% Similarity=1.082 Sum_probs=137.2
Q ss_pred CeEEEEEEcCCCCeEEEecCCCCCHHHHHHHHHHHHHHHhccCCCccceEEeCCeEEEEEEeCcEEEEEEecCCCCHHHH
Q 031317 1 MIHFVLLISRQGKVRLTKWYSPYTQKERSKVIRELSGVILTRGPKLCNFVEWRGYKVVYKRYASLYFCMCVDQEDNELEI 80 (161)
Q Consensus 1 MI~al~Iln~~G~~~l~K~Y~~~~~~~~~~~~~~i~~~i~~r~~~~~~i~~~~~~~~vy~~~~~L~f~~v~~~neNel~i 80 (161)
||++++++|++|++||+|||.+.+.++|+.+++++-+.+++|++++|++++++++++|||||++|||++++..++|||++
T Consensus 1 mi~f~LlvsrQGk~rL~k~y~~~~~~er~~i~re~i~~~Lar~pk~csfie~kd~kvVyrryasl~f~~~v~~~dNEL~~ 80 (145)
T KOG0934|consen 1 MIKFFLLVSRQGKTRLQKWYEALSIKERKKIERELIKSVLARKPKMCSFIEYKDEKVVYRRYASLFFCVGVEDNDNELAI 80 (145)
T ss_pred CeEEEEEEeccCceehhHHHhhhcHHHHHHHHHHHHHHHHhCCcccccchhccCceehhhhhhhEEEEEEEecCCchhhH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcccchhhHHhhHHHHHHHHHHHHhCcEeeecCHHHHHHHHHhhhhhH
Q 031317 81 LEIIHHYVEILDRYFGSVCELDLIFNFHKAYYILDEILIAGELQESSKKTVARLIAAQDSLV 142 (161)
Q Consensus 81 ~efL~~~ve~L~~yfg~v~E~~i~~Nf~~vy~lLDEmid~G~~~eT~~~~i~~~i~~~~~~~ 142 (161)
+|+||++||+||+|||+|||+||++||.++|.+|||++.+|.++||+....++.+..++-+.
T Consensus 81 LE~IH~~vE~lDkYFg~VCELDiiFNfekay~ILde~~~~g~~~e~~k~~~~~~i~~ad~l~ 142 (145)
T KOG0934|consen 81 LEFIHNYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEIQETSKNDVLKAIAQADLLQ 142 (145)
T ss_pred HHHHHHHHHHHHHHhccceeeEEEEehHhHHHHHHHHhcCcchHhhhcccHHHHHHHhhhcc
Confidence 99999999999999999999999999999999999999999999999998888887776543
No 4
>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=4.2e-38 Score=239.18 Aligned_cols=146 Identities=38% Similarity=0.727 Sum_probs=139.9
Q ss_pred CeEEEEEEcCCCCeEEEecCCCCCHHHHHHHHHHHHHHHhccCCCccceEEe----C--CeEEEEEEeCcEEEEEEecCC
Q 031317 1 MIHFVLLISRQGKVRLTKWYSPYTQKERSKVIRELSGVILTRGPKLCNFVEW----R--GYKVVYKRYASLYFCMCVDQE 74 (161)
Q Consensus 1 MI~al~Iln~~G~~~l~K~Y~~~~~~~~~~~~~~i~~~i~~r~~~~~~i~~~----~--~~~~vy~~~~~L~f~~v~~~n 74 (161)
||+|++|+|++|++||.|||.+.+.+.||.+.+++|..+.+|++..|+|++. + +.+++||+|+.|||+.++|+.
T Consensus 1 MI~AvlifNn~gkPRL~KFY~p~~~~~Qq~lir~vf~lvs~R~~n~~nFLe~~~l~g~~d~rlIYrhYATLYFvfvvD~s 80 (182)
T KOG0936|consen 1 MIKAVLIFNNKGKPRLVKFYTPVDEEKQQQLIREVFHLVSKRPDNVCNFLEGNSLIGGSDNRLIYRHYATLYFVFVVDSS 80 (182)
T ss_pred CeeEEEEecCCCCcceeeecCcCChHHHHHHHHHHHHHHHcCCchHhhhhccccccCCccceeehheeeeEEEEEEEcCC
Confidence 9999999999999999999999888889999999999999999999999974 3 789999999999999999999
Q ss_pred CCHHHHHHHHHHHHHHHHHHhcccchhhHHhhHHHHHHHHHHHHhCcEeeecCHHHHHHHHHhhhhhHHhhh
Q 031317 75 DNELEILEIIHHYVEILDRYFGSVCELDLIFNFHKAYYILDEILIAGELQESSKKTVARLIAAQDSLVETAK 146 (161)
Q Consensus 75 eNel~i~efL~~~ve~L~~yfg~v~E~~i~~Nf~~vy~lLDEmid~G~~~eT~~~~i~~~i~~~~~~~~~~~ 146 (161)
||||.++++||.|||+||++|.++||.|+++|+.++|.+|+|++.+|.++||+.+.|...+..+.++.|+..
T Consensus 81 EsEL~iLDLIQvfVEtLDkCF~nVcELDliF~~~k~h~iL~EiV~GGmVlETn~neIv~av~~~nkleks~~ 152 (182)
T KOG0936|consen 81 ESELGILDLIQVFVETLDKCFENVCELDLIFNWQKVHAILAEIVMGGMVLETNMNEIVAAVDEQNKLEKSED 152 (182)
T ss_pred cchhHHHHHHHHHHHHHHHHHHhhhhhhheeeHHHHHHHHHHHHhCCeEEeccHHHHHHHHHHhchhhhccC
Confidence 999999999999999999999999999999999999999999999999999999999999999998887654
No 5
>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=4.3e-38 Score=230.87 Aligned_cols=141 Identities=50% Similarity=0.962 Sum_probs=131.9
Q ss_pred CeEEEEEEcCCCCeEEEecCCCCCHHHHHHHHHHHHHHHhccCCCccceEEeCCeEEEE-EEeCcEEEEEEecCCCCHHH
Q 031317 1 MIHFVLLISRQGKVRLTKWYSPYTQKERSKVIRELSGVILTRGPKLCNFVEWRGYKVVY-KRYASLYFCMCVDQEDNELE 79 (161)
Q Consensus 1 MI~al~Iln~~G~~~l~K~Y~~~~~~~~~~~~~~i~~~i~~r~~~~~~i~~~~~~~~vy-~~~~~L~f~~v~~~neNel~ 79 (161)
||++++|+|++|++|++|||-+.+..++++++.++++.+..|+.+..++++..+.+.+| |||++|||+++++.-+|+++
T Consensus 1 mi~FILiqNr~Gk~RLak~yv~~dd~ek~~~~~~vh~lvs~Rd~K~~~~~~~~~~~~~~~rryagLyf~~~vd~tDnela 80 (143)
T KOG0935|consen 1 MIRFILIQNRAGKTRLAKWYVQFDDDEKQKLIEEVHALVTVRDAKHTNFVEFRNFKIIYRRRYAGLYFCICVDVTDNELA 80 (143)
T ss_pred CeEEEEEEccccceeheeeeeccCchHHHHHHHHHHHHHhhccchhhhheeeeeceEEEEEeeCCEEEEEEEecCCchHH
Confidence 99999999999999999999997777889999999999999998876666666666655 59999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcccchhhHHhhHHHHHHHHHHHHhCcEeeecCHHHHHHHHHhhhhh
Q 031317 80 ILEIIHHYVEILDRYFGSVCELDLIFNFHKAYYILDEILIAGELQESSKKTVARLIAAQDSL 141 (161)
Q Consensus 80 i~efL~~~ve~L~~yfg~v~E~~i~~Nf~~vy~lLDEmid~G~~~eT~~~~i~~~i~~~~~~ 141 (161)
.++-||.|||+|+.||||+||.|+++||.+||.++|||+-+|.++||++..+++|+.+.+++
T Consensus 81 yLe~IHlFVEvLd~fF~NVCELDlvFNFyKVy~i~DEm~l~GEi~Etsk~~vlerl~~L~~L 142 (143)
T KOG0935|consen 81 YLEHIHLFVEVLDEFFHNVCELDLVFNFYKVYTIVDEMFLAGEIRETSKTKVLERLLMLQSL 142 (143)
T ss_pred HHHHHHHHHHHHHHHhccccceeeeeeeeeHHHHHHHHHHhhhhhhhhHHHHHHHHHHHhcc
Confidence 99999999999999999999999999999999999999999999999999999999998875
No 6
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.97 E-value=5.2e-31 Score=222.22 Aligned_cols=134 Identities=19% Similarity=0.256 Sum_probs=123.8
Q ss_pred CeEEEEEEcCCCCeEEEecCCCCCHHHHHHHHHHHHHH-HhccCCCccceEEeCCeEEEEEEeCcEEEEEEecCCCCHHH
Q 031317 1 MIHFVLLISRQGKVRLTKWYSPYTQKERSKVIRELSGV-ILTRGPKLCNFVEWRGYKVVYKRYASLYFCMCVDQEDNELE 79 (161)
Q Consensus 1 MI~al~Iln~~G~~~l~K~Y~~~~~~~~~~~~~~i~~~-i~~r~~~~~~i~~~~~~~~vy~~~~~L~f~~v~~~neNel~ 79 (161)
||+++||+|.+|+++|.|.||+. -++-.-++|+. +++..+..||++.+++++|+|.|..+||+++++++|.|.++
T Consensus 1 misglfi~n~rGevlink~fr~d----lkrs~~diFRv~vi~n~d~r~PV~~igsttf~~~r~~nl~lvaitksN~Nva~ 76 (446)
T KOG0938|consen 1 MISGLFIYNLRGEVLINKTFRDD----LKRSIVDIFRVQVINNLDVRSPVLTIGSTTFHHIRSSNLWLVAITKSNANVAA 76 (446)
T ss_pred CcceEEEEeccCcEEEehhhhhh----hhhhHHHHHHHhhhhccccCCCeeEecceeEEEEeeccEEEEEEecCCCchhh
Confidence 99999999999999999999983 34556677877 77776679999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcccchhhHHhhHHHHHHHHHHHHhCcEeeecCHHHHHHHHHhh
Q 031317 80 ILEIIHHYVEILDRYFGSVCELDLIFNFHKAYYILDEILIAGELQESSKKTVARLIAAQ 138 (161)
Q Consensus 80 i~efL~~~ve~L~~yfg~v~E~~i~~Nf~~vy~lLDEmid~G~~~eT~~~~i~~~i~~~ 138 (161)
++|||+.++.+|.+|||..+|+.|++||+++||+||||+|+|+||+|+|+.++..++.+
T Consensus 77 v~eFl~kl~avm~aYfgk~~Eeaiknnf~lI~ElLDemld~G~pqnte~~al~~~is~~ 135 (446)
T KOG0938|consen 77 VFEFLYKLDAVMNAYFGKDREEAIKNNFVLIYELLDEMLDFGIPQNTEPNALKAQISQK 135 (446)
T ss_pred HHHHHHHHHHHHHHHhcccchhhhhhceEeHHHHHHHHHhcCCCccCChhHHHhhhhhh
Confidence 99999999999999999999999999999999999999999999999999877777654
No 7
>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.96 E-value=1.5e-28 Score=187.99 Aligned_cols=135 Identities=24% Similarity=0.377 Sum_probs=124.3
Q ss_pred eEEEEEEcCCCCeEEEecCCC--CC-HHHHHHHHHHHHHHHhccCCCccceEEeCCeEEEEEEeCcEEEEEEecCCCCHH
Q 031317 2 IHFVLLISRQGKVRLTKWYSP--YT-QKERSKVIRELSGVILTRGPKLCNFVEWRGYKVVYKRYASLYFCMCVDQEDNEL 78 (161)
Q Consensus 2 I~al~Iln~~G~~~l~K~Y~~--~~-~~~~~~~~~~i~~~i~~r~~~~~~i~~~~~~~~vy~~~~~L~f~~v~~~neNel 78 (161)
+++++|+|++|+|+++|||.+ ++ -++|+++|+.+|.++.+ ..+.|..++|..++|+..-||+|++++..+|||+
T Consensus 9 vk~iliLD~~G~Ri~aKYY~~~~~s~vkeqkaFEK~lF~KT~k---t~~eI~~ldg~~vvYk~~~Dl~fyv~G~~~ENEl 85 (175)
T KOG3343|consen 9 VKAILILDSDGKRILAKYYDDPHPSTVKEQKAFEKNLFSKTSK---TESEILLLDGNTVVYKSVIDLHFYVVGSEEENEL 85 (175)
T ss_pred hheEEEEcCCCCEeeeeecCCCcchhHHHHHHHHHHHhccccc---ccceeEEecCcEEEEEecccEEEEEecCcchhHH
Confidence 679999999999999999997 44 67899999999988854 3567889999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhcc-cchhhHHhhHHHHHHHHHHHHhCcEeeecCHHHHHHHHHhhh
Q 031317 79 EILEIIHHYVEILDRYFGS-VCELDLIFNFHKAYYILDEILIAGELQESSKKTVARLIAAQD 139 (161)
Q Consensus 79 ~i~efL~~~ve~L~~yfg~-v~E~~i~~Nf~~vy~lLDEmid~G~~~eT~~~~i~~~i~~~~ 139 (161)
++.+.|+++.+++...|.. +....+.+|++.+...+|||+|+|.++||+|+.|..|+....
T Consensus 86 ~L~svL~~l~dal~llLr~nveKr~llEN~D~i~L~~DEiiD~GvILEtdp~~ia~rv~~~~ 147 (175)
T KOG3343|consen 86 MLMSVLTCLFDALSLLLRKNVEKRELLENLDLIFLALDEIIDGGVILETDPNQIAQRVALRP 147 (175)
T ss_pred HHHHHHHHHHHHHHHHHHhChhHHHHHhhhccceeehhhhccCceEEecCHHHHHHHhccCC
Confidence 9999999999999999976 666799999999999999999999999999999999998643
No 8
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.90 E-value=3e-23 Score=179.79 Aligned_cols=134 Identities=16% Similarity=0.276 Sum_probs=116.4
Q ss_pred eEEEEEEcCCCCeEEEecCCCCCHHHHHHHHHHHHHHHhcc--CCCccceEEeCCeEEEEEEeCcEEEEEEecCCCCHHH
Q 031317 2 IHFVLLISRQGKVRLTKWYSPYTQKERSKVIRELSGVILTR--GPKLCNFVEWRGYKVVYKRYASLYFCMCVDQEDNELE 79 (161)
Q Consensus 2 I~al~Iln~~G~~~l~K~Y~~~~~~~~~~~~~~i~~~i~~r--~~~~~~i~~~~~~~~vy~~~~~L~f~~v~~~neNel~ 79 (161)
++|+|++|.+|+++++|.||+..+. .....++++.... .+..+|++.++|..++|.+++++|++++++.|.|+..
T Consensus 1 ~sa~fild~~G~~lisr~yr~dv~~---s~~~~F~~~l~~~e~~~~~~p~l~~~g~~~~~ik~s~lylv~~~~~n~~a~~ 77 (424)
T KOG0937|consen 1 ASAVFILDHKGEVLISRDYRGDVPM---SSTEKFFRKLFEKEEGDESPPFLVHDGSRFIHIKHSNLYLVAGTRPNVSAAL 77 (424)
T ss_pred CceEEEEcCCCcEeEeecccccCCh---hhhhhHHHHHhhhcccCCCCCeEEeCCceEEEEeecceEEEEEeccCCCHHH
Confidence 5899999999999999999984321 2234444443232 3457999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcccchhhHHhhHHHHHHHHHHHHhCcEeeecCHHHHHHHHHhh
Q 031317 80 ILEIIHHYVEILDRYFGSVCELDLIFNFHKAYYILDEILIAGELQESSKKTVARLIAAQ 138 (161)
Q Consensus 80 i~efL~~~ve~L~~yfg~v~E~~i~~Nf~~vy~lLDEmid~G~~~eT~~~~i~~~i~~~ 138 (161)
+++||+++++++.+||+.+.|+.+++||+++||+|||++|+||||.|+++.+.++++..
T Consensus 78 v~~~l~~~~~v~~~y~~~l~e~si~~n~vlvyElLde~mDFGypQ~t~s~iL~~yi~~~ 136 (424)
T KOG0937|consen 78 VLSFLYAVADVFGDYLSELEEESIRDNFVLVYELLDEVMDFGYPQTTDSEILKNYITQK 136 (424)
T ss_pred HHHHHHHHHHHHHHHhccCCccceecchHHHHHHHHHHhccCCcccchHHHHHHHhccc
Confidence 99999999999999999999999999999999999999999999999999777777655
No 9
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.90 E-value=1.4e-23 Score=178.30 Aligned_cols=140 Identities=21% Similarity=0.252 Sum_probs=118.4
Q ss_pred CeEEEEEEcCCCCeEEEecCCCCCHHHHHHHHHHHHHHHhcc--CCCccceEEeCCeEEEEEEeCcEEEEEEecCCCCHH
Q 031317 1 MIHFVLLISRQGKVRLTKWYSPYTQKERSKVIRELSGVILTR--GPKLCNFVEWRGYKVVYKRYASLYFCMCVDQEDNEL 78 (161)
Q Consensus 1 MI~al~Iln~~G~~~l~K~Y~~~~~~~~~~~~~~i~~~i~~r--~~~~~~i~~~~~~~~vy~~~~~L~f~~v~~~neNel 78 (161)
||.++|+.|.+|+++++|++++-... +.+++.+|..-.+. .+..+|++..+.|++.-.-..++||++++..+..||
T Consensus 1 mi~siflidtsg~l~lek~~~g~t~~--rsic~~f~e~~~~~~~~e~~ppvi~~p~hylfsv~~~~i~~~~~st~e~pPL 78 (418)
T KOG2740|consen 1 MILSIFLIDTSGDLLLEKHLKGSTVV--RSICDYFFEDQSSDDDLEHVPPVISTPHHYLFSVYRDLIFFCAVSTVETPPL 78 (418)
T ss_pred CeeEEEEEcCCchhhhhHhhCCceee--eehHHHHHHhhhhccccccCCceecCCceeeeeeeccCcEEEEEEeccCCCh
Confidence 99999999999999999999962221 35777777664443 355788888888988777777999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhcccchhhHHhhHHHHHHHHHHHHhCcEeeecCHHHHHHHHHhhhhhH
Q 031317 79 EILEIIHHYVEILDRYFGSVCELDLIFNFHKAYYILDEILIAGELQESSKKTVARLIAAQDSLV 142 (161)
Q Consensus 79 ~i~efL~~~ve~L~~yfg~v~E~~i~~Nf~~vy~lLDEmid~G~~~eT~~~~i~~~i~~~~~~~ 142 (161)
+++|||+|++++|..|||+++|..|++|++.||++||||+|+|+|+.|||+.+.+-+....-+.
T Consensus 79 ~~iefL~rv~dv~~eyFg~~s~~~Ik~N~~vv~ell~emiDnGfpl~tE~NiLke~i~pps~l~ 142 (418)
T KOG2740|consen 79 MVIEFLHRVVDVLLEYFGGLSESKIKDNVVVVYELLDEMIDNGFPLVTEPNILKELIPPPSFLS 142 (418)
T ss_pred hHHHHHHHHHHHHHHHhcccCHhHhhcceeeHHHHHHHHHHcCCCcccChhHHHhhcCChHHHH
Confidence 9999999999999999999999999999999999999999999999999985555544443333
No 10
>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=99.82 E-value=4.1e-20 Score=141.48 Aligned_cols=133 Identities=16% Similarity=0.237 Sum_probs=121.5
Q ss_pred eEEEEEEcCCCCeEEEecCCCC-----------CHHHHHHHHHHHHHHHhccCCCccceEEeCCeEEEEEEeCcEEEEEE
Q 031317 2 IHFVLLISRQGKVRLTKWYSPY-----------TQKERSKVIRELSGVILTRGPKLCNFVEWRGYKVVYKRYASLYFCMC 70 (161)
Q Consensus 2 I~al~Iln~~G~~~l~K~Y~~~-----------~~~~~~~~~~~i~~~i~~r~~~~~~i~~~~~~~~vy~~~~~L~f~~v 70 (161)
+.|++|+|++|++++.|||.++ +-++++.+++.+++++.+. +..++.+.++.++|+++.++.|+.+
T Consensus 8 v~a~LilDsqGeriy~kyy~pph~~eg~~~vFnsvkkekefek~l~eKt~k~---~~~Il~f~d~lV~~k~~~dv~~yiv 84 (187)
T COG5541 8 VEALLILDSQGERIYRKYYQPPHRSEGHQLVFNSVKKEKEFEKKLAEKTAKD---RESILMFYDRLVMCKRLDDVLLYIV 84 (187)
T ss_pred eeeeEEecCCccchhhhhcCCcccccccchhhcchhHHHHHHHHHHHHhhcC---ccceeeEcceeeeeeeehhEEEEEe
Confidence 6899999999999999999874 3446778999999887542 5679999999999999999999999
Q ss_pred ecCCCCHHHHHHHHHHHHHHHHHHhccc-chhhHHhhHHHHHHHHHHHHhCcEeeecCHHHHHHHHHh
Q 031317 71 VDQEDNELEILEIIHHYVEILDRYFGSV-CELDLIFNFHKAYYILDEILIAGELQESSKKTVARLIAA 137 (161)
Q Consensus 71 ~~~neNel~i~efL~~~ve~L~~yfg~v-~E~~i~~Nf~~vy~lLDEmid~G~~~eT~~~~i~~~i~~ 137 (161)
+.-+|||.++.+.+..+..+|...|+.. .+..+.+|++.+..++||.+|+|.++||+++.|+.|+..
T Consensus 85 ~~meeNE~~l~q~f~~ir~Al~li~k~~~dkr~v~enYDqivl~vdEtid~Gvilet~s~~ia~rv~K 152 (187)
T COG5541 85 SPMEENEPFLGQVFDEIRAALILIVKTPTDKRNVWENYDQIVLLVDETIDEGVILETKSDEIADRVPK 152 (187)
T ss_pred cccccccHHHHHHHHHHHHHHHHHHcCCcchhhHHhhhceEEEeeehhcccceEeecChHHHHHhCCC
Confidence 9999999999999999999999999987 556799999999999999999999999999999999986
No 11
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.30 E-value=1.3e-05 Score=70.72 Aligned_cols=131 Identities=19% Similarity=0.331 Sum_probs=108.1
Q ss_pred eEEEEEEcCCCCeEEEecCCCCCHHHHHHHHHHH--HHHHhccCCCccceEEeCCeEEEEEEeCcEEEEEEecCCCCHHH
Q 031317 2 IHFVLLISRQGKVRLTKWYSPYTQKERSKVIREL--SGVILTRGPKLCNFVEWRGYKVVYKRYASLYFCMCVDQEDNELE 79 (161)
Q Consensus 2 I~al~Iln~~G~~~l~K~Y~~~~~~~~~~~~~~i--~~~i~~r~~~~~~i~~~~~~~~vy~~~~~L~f~~v~~~neNel~ 79 (161)
.-+.-+.+.+|+.+++|.|+.++. .+++.-+ |.+..+ ..++.-+++.+++++||.=..++|++.+|.-+-|-|-
T Consensus 3 vlaa~i~t~~Gk~ivsRqf~~Msr---~RIEgLl~aFpkLv~-~~~qhT~vEt~~VRYVYqP~d~lY~vLITtk~SNIle 78 (512)
T KOG2635|consen 3 VLAASINTKTGKAIVSRQFREMSR---SRIEGLLAAFPKLVS-AGKQHTFVETDSVRYVYQPLDNLYIVLITTKQSNILE 78 (512)
T ss_pred EEEEEEeecCCceeeehHhHhhhH---HHHHHHHHHhHHhhc-cCCCccEEecccEEEEEEecccEEEEEEeccccchhh
Confidence 346678899999999999998754 3555554 444433 2346779999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhcccchhhHHhhHHHHHHHHHHHHhCcEeeecCHHHHHHHHH
Q 031317 80 ILEIIHHYVEILDRYFGSVCELDLIFNFHKAYYILDEILIAGELQESSKKTVARLIA 136 (161)
Q Consensus 80 i~efL~~~ve~L~~yfg~v~E~~i~~Nf~~vy~lLDEmid~G~~~eT~~~~i~~~i~ 136 (161)
-++.|+.|..+.-.|+..+.|+.|.+|-=.+...+||++-=||=-..+...|..+..
T Consensus 79 Dl~TL~Lfskvipey~~slde~eI~~~~FelifAFDEivsLGyre~v~laQikty~e 135 (512)
T KOG2635|consen 79 DLETLRLFSKVIPEYCSSLDEKEILENAFELIFAFDEIVSLGYRENVNLAQIKTYLE 135 (512)
T ss_pred HHHHHHHHHHhchhhhhhhhHHHHHHhhhhhhhccchhhhhcccccccHHHhhhhhc
Confidence 999999999999999999999999999767778899999999766666555555443
No 12
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=97.42 E-value=0.014 Score=46.57 Aligned_cols=77 Identities=17% Similarity=0.241 Sum_probs=69.6
Q ss_pred CeEEEEEEeCcEEEEEEecCCCCHHHHHHHHHHHHHHHHHHhcccch-hhHHhhHHHHHHHHHHHHhCcEeeecCHHH
Q 031317 54 GYKVVYKRYASLYFCMCVDQEDNELEILEIIHHYVEILDRYFGSVCE-LDLIFNFHKAYYILDEILIAGELQESSKKT 130 (161)
Q Consensus 54 ~~~~vy~~~~~L~f~~v~~~neNel~i~efL~~~ve~L~~yfg~v~E-~~i~~Nf~~vy~lLDEmid~G~~~eT~~~~ 130 (161)
...++|....++.|..|+++.||-++.-.+|..++..|.++|..+.- ..+...-+.|..+|+..+=.|-.+--+.+.
T Consensus 103 ~k~vvW~~v~~l~ftLVce~hEN~lLa~~~L~~~~~~l~~~~~~l~~~~e~l~k~d~i~aiL~~fLP~GQLLFlN~~~ 180 (189)
T PF15001_consen 103 PKIVVWLGVGSLCFTLVCEPHENRLLAENTLRLFIRHLLEHLKILSQPSEVLLKSDRILAILHRFLPHGQLLFLNHRF 180 (189)
T ss_pred CcEEEeeccCCEEEEEEecCchhHHHHHHHHHHHHHHHHHHHHHhCcHHHhhhhHHHHHHHHHHhCCCCcEEEEcHHH
Confidence 46779999999999999999999999999999999999999977544 567779999999999999999999888873
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=96.18 E-value=0.18 Score=44.65 Aligned_cols=90 Identities=9% Similarity=0.148 Sum_probs=58.5
Q ss_pred EEEEEEcCCCCeEEEecCCCCCHHHHHHHHHHHHHHHhc--cCCCccceEEeCCeEEEEEEeCcEEEEEEecCCCCHHHH
Q 031317 3 HFVLLISRQGKVRLTKWYSPYTQKERSKVIRELSGVILT--RGPKLCNFVEWRGYKVVYKRYASLYFCMCVDQEDNELEI 80 (161)
Q Consensus 3 ~al~Iln~~G~~~l~K~Y~~~~~~~~~~~~~~i~~~i~~--r~~~~~~i~~~~~~~~vy~~~~~L~f~~v~~~neNel~i 80 (161)
+-+||+.+.||+++++| +. ...-..+..-+...+.. ..++.---+..+++++++...+.|+++++++..|++..+
T Consensus 12 kh~fIlS~AGKPIysr~--G~-e~~l~~~~g~~~aiiS~~~~~~d~l~~i~~~~~~ivfl~r~pl~lv~vS~~~e~~~~l 88 (415)
T PF03164_consen 12 KHFFILSSAGKPIYSRY--GD-EDKLSSLMGVIQAIISFFQSNGDELRSIRAGDHRIVFLNRGPLILVAVSKTGESESQL 88 (415)
T ss_pred CeEEEECCCCceeEEec--CC-hHHHHHHHHHHHHHHHHHHhCCCcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCHHHH
Confidence 35899999999999998 32 11122233333333221 112233344679999999999999999999999997776
Q ss_pred HHHHHHHHHHHHHHh
Q 031317 81 LEIIHHYVEILDRYF 95 (161)
Q Consensus 81 ~efL~~~ve~L~~yf 95 (161)
..-|..+...+-..+
T Consensus 89 ~~qL~~ly~qils~l 103 (415)
T PF03164_consen 89 RKQLDYLYSQILSIL 103 (415)
T ss_pred HHHHHHHHHHHHHhc
Confidence 665555554444333
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=95.43 E-value=0.32 Score=36.05 Aligned_cols=92 Identities=15% Similarity=0.192 Sum_probs=63.0
Q ss_pred eEEEEEEcCCCCeEEEecCCC-CCHHHHHHHHHHHH---HHHhccC--CCccceEEeCCeEEEEEEeCcEEEEEEecCCC
Q 031317 2 IHFVLLISRQGKVRLTKWYSP-YTQKERSKVIRELS---GVILTRG--PKLCNFVEWRGYKVVYKRYASLYFCMCVDQED 75 (161)
Q Consensus 2 I~al~Iln~~G~~~l~K~Y~~-~~~~~~~~~~~~i~---~~i~~r~--~~~~~i~~~~~~~~vy~~~~~L~f~~v~~~ne 75 (161)
+.+++|-|++|=+++.=.... +...-++.+...+- .+..+-+ ....-+..++++.+++.....+|+.+++.++.
T Consensus 17 l~~I~itDrDGvpi~~v~~~~~~~~~~~~~~~~tf~~a~~Q~~KL~lG~nk~ii~~Y~~~qvv~~~~~pl~it~ias~~a 96 (119)
T PF08923_consen 17 LQAIVITDRDGVPIAKVSSDSAPESAMRPSLLSTFAMAIDQASKLGLGKNKSIIAYYDSYQVVQFNKLPLYITFIASSNA 96 (119)
T ss_dssp EEEEEEEETTS-EEEEEE-TTS-GGGGSHHHHCCHHHHHHHHTTSSS-SEEEEEEEESSEEEEEEEETTEEEEEEEETTS
T ss_pred eEEEEEECCCCcEEEEecCCCCcchhhhhHHHHHHHHHhhcccccCCCCceEEEEEeCCEEEEEEeCCCeEEEEEecCCC
Confidence 578999999999988755444 22222334443321 1222211 23455778999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHHHH
Q 031317 76 NELEILEIIHHYVEILDR 93 (161)
Q Consensus 76 Nel~i~efL~~~ve~L~~ 93 (161)
|--+++.+-+.+...|..
T Consensus 97 N~G~il~l~~~L~~~l~~ 114 (119)
T PF08923_consen 97 NTGLILSLEEELAPILNE 114 (119)
T ss_dssp -HHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHhHHHHHHHHHH
Confidence 999999998888887764
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=95.19 E-value=0.35 Score=36.63 Aligned_cols=95 Identities=20% Similarity=0.297 Sum_probs=57.2
Q ss_pred eEEEEEEcCCCCeEEEecCCCC--------CHHHHHHHHHHHHHH--Hh-ccCC--------Cccce--EEeCCeEE-EE
Q 031317 2 IHFVLLISRQGKVRLTKWYSPY--------TQKERSKVIRELSGV--IL-TRGP--------KLCNF--VEWRGYKV-VY 59 (161)
Q Consensus 2 I~al~Iln~~G~~~l~K~Y~~~--------~~~~~~~~~~~i~~~--i~-~r~~--------~~~~i--~~~~~~~~-vy 59 (161)
|..++|+|+.|..+..|-|... +..+++.+..-+|-. +. +-+. ..+.+ +..+.+++ .|
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 6789999999999999988652 234455555555422 11 1111 11223 45678888 46
Q ss_pred EEeCcEEEEEEecCCCCHHHHHHHHHHHHHHHHHHh-cc
Q 031317 60 KRYASLYFCMCVDQEDNELEILEIIHHYVEILDRYF-GS 97 (161)
Q Consensus 60 ~~~~~L~f~~v~~~neNel~i~efL~~~ve~L~~yf-g~ 97 (161)
..-.++-|++++|.+...+ .-++++.+.++.-+|- +|
T Consensus 81 eT~TGlKFvl~td~~~~~~-~~~l~~~~~~lY~dyV~KN 118 (142)
T PF04099_consen 81 ETPTGLKFVLITDPNVPSL-RDELLRIYYELYVDYVVKN 118 (142)
T ss_dssp E-TTS-EEEEEE-TTCCHC-HHHHHHHHHHHHHHHHHS-
T ss_pred EcCcCcEEEEEecCCCccH-HHHHHHHHHHHHHHHHhhC
Confidence 6688899999999998653 5567788888887774 44
No 16
>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=93.20 E-value=0.91 Score=30.66 Aligned_cols=48 Identities=10% Similarity=0.106 Sum_probs=43.2
Q ss_pred eEEeCCeEEEEEEeCcEEEEEEecCCCCHHHHHHHHHHHHHHHHHHhc
Q 031317 49 FVEWRGYKVVYKRYASLYFCMCVDQEDNELEILEIIHHYVEILDRYFG 96 (161)
Q Consensus 49 i~~~~~~~~vy~~~~~L~f~~v~~~neNel~i~efL~~~ve~L~~yfg 96 (161)
.++.+++.+-|...+++.++++++.+-+.-..+.||..+.+-+..-++
T Consensus 18 s~~~~~~~fh~~~~~~i~~~citd~~~~~r~aF~fL~~i~~~F~~~~~ 65 (83)
T PF13774_consen 18 SYESGNYVFHYLVEDGIAYLCITDKSYPKRVAFAFLEEIKQEFIQTYG 65 (83)
T ss_dssp EEEETTEEEEEEEETTEEEEEEEETTS-HHHHHHHHHHHHHHHHHHCT
T ss_pred EEEECCEEEEEEEcCCeEEEEEEcCCCCcchHHHHHHHHHHHHHHHcC
Confidence 456899999999999999999999999999999999999999988887
No 17
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=91.93 E-value=3.8 Score=33.23 Aligned_cols=89 Identities=12% Similarity=0.141 Sum_probs=63.7
Q ss_pred EEEEcCCCCeEEEecCCC-CCHHHHHHHHHHHHHHHhccCCCccceEEeCCeEEEEEEeCcEEEEEEecCCCCHHHHHHH
Q 031317 5 VLLISRQGKVRLTKWYSP-YTQKERSKVIRELSGVILTRGPKLCNFVEWRGYKVVYKRYASLYFCMCVDQEDNELEILEI 83 (161)
Q Consensus 5 l~Iln~~G~~~l~K~Y~~-~~~~~~~~~~~~i~~~i~~r~~~~~~i~~~~~~~~vy~~~~~L~f~~v~~~neNel~i~ef 83 (161)
++=+=.+|-++|++|=.- -+ -..+.+.+-.++-..++ .---...|+|.|-|.+-+++.++++++.+..--.-+.|
T Consensus 4 iYs~VARGTvvLaeft~~~gN---f~sva~qiL~klp~~~n-~k~tYs~d~y~Fh~l~~dg~tylcvadds~gR~ipfaF 79 (217)
T KOG0859|consen 4 IYSFVARGTVILAEFTEFSGN---FSSIAAQILQKLPSSSN-SKFTYSCDGYTFHYLVEDGLTYLCVADDSAGRQIPFAF 79 (217)
T ss_pred eEEEEecceEEEEeeeeccCC---HHHHHHHHHHhCCCCCC-CceEEecCCeEEEEEEeCCeEEEEEEeccccccccHHH
Confidence 344557899999996432 11 12345555555533322 11134579999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhcc
Q 031317 84 IHHYVEILDRYFGS 97 (161)
Q Consensus 84 L~~~ve~L~~yfg~ 97 (161)
|.++-+-+.+-+|.
T Consensus 80 Le~Ik~~F~k~YG~ 93 (217)
T KOG0859|consen 80 LERIKEDFKKRYGG 93 (217)
T ss_pred HHHHHHHHHHHhcc
Confidence 99998887776665
No 18
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=89.88 E-value=4.3 Score=33.11 Aligned_cols=74 Identities=11% Similarity=0.183 Sum_probs=58.6
Q ss_pred HHHHHHHHHHHHHHhccCCCccceEEeCCeEEEEEEeCcEEEEEEecCCCCHHHHHHHHHHHHHHHHHHhcccch
Q 031317 26 KERSKVIRELSGVILTRGPKLCNFVEWRGYKVVYKRYASLYFCMCVDQEDNELEILEIIHHYVEILDRYFGSVCE 100 (161)
Q Consensus 26 ~~~~~~~~~i~~~i~~r~~~~~~i~~~~~~~~vy~~~~~L~f~~v~~~neNel~i~efL~~~ve~L~~yfg~v~E 100 (161)
.+.++-.+.++++....+...|.+ +.+++.|.|.-..++++++.++.+-+--+.+.+|..+.+-+.+-+|.-++
T Consensus 31 ~e~r~q~K~L~kkLs~~s~~r~Si-etg~f~fHfli~~~Vcylvicd~~yP~kLAF~YLedL~~EF~~~~~~~~~ 104 (216)
T KOG0862|consen 31 LEYRQQAKSLFKKLSQQSPTRCSI-ETGPFVFHFLIESGVCYLVICDKSYPRKLAFSYLEDLAQEFDKSYGKNII 104 (216)
T ss_pred HHHHHHHHHHHHhccCCCCccccc-ccCCeEEEEEecCCEEEEEEecCCCcHHHHHHHHHHHHHHHHHhcccccC
Confidence 445555667777664433334444 56889999999999999999999999999999999999999998886433
No 19
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=85.18 E-value=6.6 Score=29.19 Aligned_cols=91 Identities=16% Similarity=0.314 Sum_probs=55.2
Q ss_pred eEEEEEEcCCCCeEEEecCCCCC----HHHHHHHHHHHHHH--Hhc-cCC--Cccc--eEEeCCeEE-EEEEeCcEEEEE
Q 031317 2 IHFVLLISRQGKVRLTKWYSPYT----QKERSKVIRELSGV--ILT-RGP--KLCN--FVEWRGYKV-VYKRYASLYFCM 69 (161)
Q Consensus 2 I~al~Iln~~G~~~l~K~Y~~~~----~~~~~~~~~~i~~~--i~~-r~~--~~~~--i~~~~~~~~-vy~~~~~L~f~~ 69 (161)
+.+++|+|+.|-.++.|-|.... ..|-.-+...++.. +.+ ... ..++ ++..+.... +|+...++-|++
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 68999999999999999985421 11110011222211 111 111 1122 445666554 899999999999
Q ss_pred Ee-cCCCCHHHHHHHHHHHHHHHHHHh
Q 031317 70 CV-DQEDNELEILEIIHHYVEILDRYF 95 (161)
Q Consensus 70 v~-~~neNel~i~efL~~~ve~L~~yf 95 (161)
++ +.-.|.++- ++.+.....+|-
T Consensus 83 ~~~k~t~na~~q---l~kiY~lYsdYV 106 (134)
T COG5122 83 VAEKRTVNALFQ---LQKIYSLYSDYV 106 (134)
T ss_pred EecCCchhHHHH---HHHHHHHHHHHh
Confidence 99 666776655 566777777765
No 20
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=83.23 E-value=24 Score=32.54 Aligned_cols=113 Identities=14% Similarity=0.178 Sum_probs=70.6
Q ss_pred CeEEEEEEcCCCCeEEEecCCCCCHHHHHHHHHHHHHH-HhccCCCccceEEeCCeEEEEEEeCc--EEEEEEecCCCCH
Q 031317 1 MIHFVLLISRQGKVRLTKWYSPYTQKERSKVIRELSGV-ILTRGPKLCNFVEWRGYKVVYKRYAS--LYFCMCVDQEDNE 77 (161)
Q Consensus 1 MI~al~Iln~~G~~~l~K~Y~~~~~~~~~~~~~~i~~~-i~~r~~~~~~i~~~~~~~~vy~~~~~--L~f~~v~~~neNe 77 (161)
||-.+.|+++.|.++...-=-+.+.++ ....+++. ++.+.+...+ +.++.+++=|...++ +.|+++-..--+=
T Consensus 1 Mld~faIFtkgG~vLw~~~~~~~~~~~---~in~lI~~~ll~er~~~~~-~~~~~yTlk~q~~N~~~lvfvvvfqki~~L 76 (587)
T KOG0781|consen 1 MLDQFAIFTKGGLVLWCYQEVGDNLKG---PINALIRSVLLSERGGVNS-FTFEAYTLKYQLDNQYSLVFVVVFQKILTL 76 (587)
T ss_pred CcceeeeecCCcEEEEEecccchhccc---hHHHHHHHHHHHhhcCccc-CchhheeEeeeecCCccEEEEEEEeccchh
Confidence 899999999999877654322233222 23444444 3333333333 677889888877665 5566666555555
Q ss_pred HHHHHHHHHHHHHHHHHhcccchhhHHhh-HHHHHHHHHHH
Q 031317 78 LEILEIIHHYVEILDRYFGSVCELDLIFN-FHKAYYILDEI 117 (161)
Q Consensus 78 l~i~efL~~~ve~L~~yfg~v~E~~i~~N-f~~vy~lLDEm 117 (161)
..+-.+|....+.+..-|...+-..+.-| ++...++|++-
T Consensus 77 ~yv~~ll~~v~~~f~e~~~~~~~~~l~~n~~~~~~e~lk~r 117 (587)
T KOG0781|consen 77 TYVDKLLNDVLNLFREKYDTQSALSLLNNTFDFQEELLKLR 117 (587)
T ss_pred hhHHHHHHHHHHHHHHHhccchHHHhhhhhHHHHHHHHHHh
Confidence 55666887777777777766555666666 55677777643
No 21
>KOG0997 consensus Uncharacterized conserved protein Sand [Function unknown]
Probab=82.88 E-value=18 Score=33.00 Aligned_cols=72 Identities=15% Similarity=0.206 Sum_probs=48.7
Q ss_pred EEEEEcCCCCeEEEecCCCC----CHHHHHHHHHHHHHHHhccCCCccceEEeCCeEEEEEEeCcEEEEEEecCCCCHHH
Q 031317 4 FVLLISRQGKVRLTKWYSPY----TQKERSKVIRELSGVILTRGPKLCNFVEWRGYKVVYKRYASLYFCMCVDQEDNELE 79 (161)
Q Consensus 4 al~Iln~~G~~~l~K~Y~~~----~~~~~~~~~~~i~~~i~~r~~~~~~i~~~~~~~~vy~~~~~L~f~~v~~~neNel~ 79 (161)
-+||+...|++++++|=... +..-.++++..+. .....-+ .+...|+++++-+.+-|+++|++..+.++--
T Consensus 119 hifilseaGKPiyS~~gs~e~l~stmGv~~alISf~q----~~~~~i~-si~a~g~k~vfl~kspl~LvA~s~t~~Sa~q 193 (523)
T KOG0997|consen 119 HIFILSEAGKPIYSRHGSDEALSSTMGVMQALISFFQ----VSGLAIT-SIHAFGNKLVFLQKSPLLLVAVSRTSQSAAQ 193 (523)
T ss_pred eEEEEecCCCceeeecCcHHHHHHHHHHHHHHHHHHh----hCCceEE-EEEecCceEEEEecCcEEEEEEcccccCHHH
Confidence 48999999999999985431 1222233333322 1112223 3457899999999999999999998887654
Q ss_pred H
Q 031317 80 I 80 (161)
Q Consensus 80 i 80 (161)
+
T Consensus 194 L 194 (523)
T KOG0997|consen 194 L 194 (523)
T ss_pred H
Confidence 3
No 22
>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=80.21 E-value=5.5 Score=30.85 Aligned_cols=58 Identities=24% Similarity=0.241 Sum_probs=44.1
Q ss_pred HHHHHHHHhcccchhhHHhhHHHHHHHHHHHHhCcEeeec------CHHHHHHHHHhhhhhHHh
Q 031317 87 YVEILDRYFGSVCELDLIFNFHKAYYILDEILIAGELQES------SKKTVARLIAAQDSLVET 144 (161)
Q Consensus 87 ~ve~L~~yfg~v~E~~i~~Nf~~vy~lLDEmid~G~~~eT------~~~~i~~~i~~~~~~~~~ 144 (161)
+-+.|+++++.+++++..+...-.-+.+||-..+|..-+- +|+.+.+.+....+..+.
T Consensus 6 fL~~L~~~L~~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG~P~~iA~~i~~~~~i~~~ 69 (181)
T PF08006_consen 6 FLNELEKYLKKLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIAREILAEYSIKEE 69 (181)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHHHHHhhhhhhh
Confidence 4566788888899999999999999999998888864443 777788887766554433
No 23
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=66.80 E-value=65 Score=25.77 Aligned_cols=45 Identities=9% Similarity=0.272 Sum_probs=35.1
Q ss_pred eEEeCCeEE-EEEEeCcEEEEEEecCCCCHHHHHHHHHHHHHHHHHHh
Q 031317 49 FVEWRGYKV-VYKRYASLYFCMCVDQEDNELEILEIIHHYVEILDRYF 95 (161)
Q Consensus 49 i~~~~~~~~-vy~~~~~L~f~~v~~~neNel~i~efL~~~ve~L~~yf 95 (161)
+++.+..++ +|....++=|+++++.-. -.+-.+|.++.+...+|-
T Consensus 125 ~LetdtF~l~~~QTlTG~KFVvis~~~~--~~aD~lLrKiYelYsDyv 170 (199)
T KOG3369|consen 125 VLETDTFTLHIFQTLTGTKFVVIAEPGT--QGADSLLRKIYELYSDYV 170 (199)
T ss_pred EEEeccEEEEEEEccCCcEEEEEecCCc--hhHHHHHHHHHHHHHHHh
Confidence 455566554 799999999999998876 456678889998888874
No 24
>KOG0861 consensus SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=60.76 E-value=86 Score=25.11 Aligned_cols=89 Identities=13% Similarity=0.148 Sum_probs=53.7
Q ss_pred eEEEEEEcCCCCeE--EEecCCC-----CCHHHHHHHHHHHHHHHhccCC--CccceEEeCCeEE-EEEEeCcEEEEEEe
Q 031317 2 IHFVLLISRQGKVR--LTKWYSP-----YTQKERSKVIRELSGVILTRGP--KLCNFVEWRGYKV-VYKRYASLYFCMCV 71 (161)
Q Consensus 2 I~al~Iln~~G~~~--l~K~Y~~-----~~~~~~~~~~~~i~~~i~~r~~--~~~~i~~~~~~~~-vy~~~~~L~f~~v~ 71 (161)
|.++.+++..+... ++.-++= .....-+.+.-++-+.+..|++ ....+ .++.+.+ +|.|..+|.-++++
T Consensus 3 i~sl~V~~~~~~~~~ll~~a~dls~FsfFqRssV~Efm~F~sktvaeRt~~g~rqsv-k~~~Y~~h~yvrndgL~~V~~~ 81 (198)
T KOG0861|consen 3 IYSLSVLHKGTSDVKLLKTASDLSSFSFFQRSSVQEFMTFISKTVAERTGPGQRQSV-KHEEYLVHVYVRNDGLCGVLIA 81 (198)
T ss_pred eEEEEEEeeCCcchhhhhhhcccccccceeeccHHHHHHHHHHHHHHhcCccccccc-ccceeEEEEEEecCCeeEEEEe
Confidence 56778888754433 3222220 1111123344444455555653 23333 4566666 79998899999999
Q ss_pred cCCCCHHHHHHHHHHHHHHH
Q 031317 72 DQEDNELEILEIIHHYVEIL 91 (161)
Q Consensus 72 ~~neNel~i~efL~~~ve~L 91 (161)
|.+-+--..+.+|+++.+-+
T Consensus 82 D~eYP~rvA~tLL~kvld~~ 101 (198)
T KOG0861|consen 82 DDEYPVRVAFTLLNKVLDEF 101 (198)
T ss_pred cCcCchhHHHHHHHHHHHHH
Confidence 99998888888887654443
No 25
>PF04086 SRP-alpha_N: Signal recognition particle, alpha subunit, N-terminal; InterPro: IPR007222 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. This entry represents the alpha subunit of the SR receptor.; GO: 0003924 GTPase activity, 0005047 signal recognition particle binding, 0005525 GTP binding, 0006184 GTP catabolic process, 0006886 intracellular protein transport, 0005785 signal recognition particle receptor complex; PDB: 2FH5_A 2GO5_1.
Probab=60.20 E-value=92 Score=25.57 Aligned_cols=50 Identities=6% Similarity=0.109 Sum_probs=35.7
Q ss_pred eEEeCCeEEEEEEeCc--EEEEEEecCCCCHHHHHHHHHHHHHHHHHHhccc
Q 031317 49 FVEWRGYKVVYKRYAS--LYFCMCVDQEDNELEILEIIHHYVEILDRYFGSV 98 (161)
Q Consensus 49 i~~~~~~~~vy~~~~~--L~f~~v~~~neNel~i~efL~~~ve~L~~yfg~v 98 (161)
-+.+++|++-|...++ |+|+||-..=-.-+.+-+||..+...|...|++.
T Consensus 21 ~~~~d~y~lkw~~~Ne~~LvfVvvYq~il~l~yvd~LL~~v~~~F~~~y~~~ 72 (279)
T PF04086_consen 21 SFTYDNYTLKWTLDNELGLVFVVVYQKILQLTYVDKLLDDVKKEFVKLYKNQ 72 (279)
T ss_dssp -------EEEEEEETTTTEEEEEEES-GGGHHHHHHHHHHHHHHHHHHTHHH
T ss_pred ceeEcCEEEEEEEeccCCEEEeeeecccccchHHHHHHHHHHHHHHHHHhHH
Confidence 3678999999988776 8899998888888888889999888888888764
No 26
>COG3322 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]
Probab=49.13 E-value=16 Score=31.15 Aligned_cols=22 Identities=18% Similarity=0.277 Sum_probs=19.4
Q ss_pred eEEEEEEcCCCCeEEEecCCCC
Q 031317 2 IHFVLLISRQGKVRLTKWYSPY 23 (161)
Q Consensus 2 I~al~Iln~~G~~~l~K~Y~~~ 23 (161)
..++|++|.+|+++++|.+++.
T Consensus 104 ~d~vf~vd~~G~~vy~~~~d~~ 125 (295)
T COG3322 104 LDGVFVVDPSGKLVYSKLVDQE 125 (295)
T ss_pred ccEEEEECCCCCEEEEeeeccc
Confidence 3589999999999999999763
No 27
>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=41.15 E-value=94 Score=22.62 Aligned_cols=21 Identities=19% Similarity=0.510 Sum_probs=17.4
Q ss_pred eEEEEEEcCCCCeEE--EecCCC
Q 031317 2 IHFVLLISRQGKVRL--TKWYSP 22 (161)
Q Consensus 2 I~al~Iln~~G~~~l--~K~Y~~ 22 (161)
+.+++++|.+|+++. .+.+..
T Consensus 50 ~d~~~~~d~~g~~~~~~~~~~~~ 72 (161)
T PF05228_consen 50 LDLIFILDPDGRVLYSSSKGYDF 72 (161)
T ss_pred ccEEEEEcCCCCEEEEeccCccc
Confidence 468999999999998 666654
No 28
>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=40.36 E-value=26 Score=17.93 Aligned_cols=18 Identities=28% Similarity=0.336 Sum_probs=14.9
Q ss_pred hhHHHHHHHHHHHHhCcE
Q 031317 105 FNFHKAYYILDEILIAGE 122 (161)
Q Consensus 105 ~Nf~~vy~lLDEmid~G~ 122 (161)
.+++.+..+++||.+.|.
T Consensus 14 ~~~~~a~~~~~~M~~~g~ 31 (31)
T PF01535_consen 14 GQFEEALEVFDEMRERGI 31 (31)
T ss_pred chHHHHHHHHHHHhHCcC
Confidence 457889999999998874
No 29
>PF09201 SRX: SRX; InterPro: IPR015284 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. This entry represents a homologue of the alpha subunit of the SR receptor. Members of this entry consist of a central six-stranded anti-parallel beta-sheet sandwiched by helix alpha1 on one side and helices alpha2-alpha4 on the other. They interact with the small GTPase SR-beta, forming a complex that matches a class of small G protein-effector complexes, including Rap-Raf, Ras-PI3K(gamma), Ras-RalGDS, and Arl2-PDE(delta) []. ; PDB: 1NRJ_A.
Probab=40.06 E-value=1.7e+02 Score=22.48 Aligned_cols=70 Identities=14% Similarity=0.297 Sum_probs=31.9
Q ss_pred CeEEEEEEcCCCCeEEEecCCC--CCHHHHHHHHHHHHHHHhcc---C--CCccceEEe-------CCeEEEEEE--eCc
Q 031317 1 MIHFVLLISRQGKVRLTKWYSP--YTQKERSKVIRELSGVILTR---G--PKLCNFVEW-------RGYKVVYKR--YAS 64 (161)
Q Consensus 1 MI~al~Iln~~G~~~l~K~Y~~--~~~~~~~~~~~~i~~~i~~r---~--~~~~~i~~~-------~~~~~vy~~--~~~ 64 (161)
|+-.+-|+..+|++++.--=-+ .+.. ++-+.+-+.+.+. + +....++.+ ++++..|.- ...
T Consensus 1 MfdQlaIFTpqGqvLyqyN~~gKKFsE~---QiN~FIs~lItsP~~~~e~~~~~k~~~i~s~~~~~~~f~~mfh~sKQPe 77 (148)
T PF09201_consen 1 MFDQLAIFTPQGQVLYQYNCLGKKFSET---QINAFISHLITSPVTKKEDSSKSKFLTISSEKKNSRSFSAMFHISKQPE 77 (148)
T ss_dssp ---EEEEE-TT-BEEEEEETTS----HH---HHHHHHHHHHHS---GGGTT--EEEEE-----------EEEEEEETTTT
T ss_pred CcceeEEeccCceEEEEecccchHHHHH---HHHHHHHHHhcCCCcccCCCcceeeEEecccccCCCChheeeeecCCCc
Confidence 8999999999999987532111 2221 2333333333321 1 123444444 377776543 567
Q ss_pred EEEEEEecC
Q 031317 65 LYFCMCVDQ 73 (161)
Q Consensus 65 L~f~~v~~~ 73 (161)
|||++.-.+
T Consensus 78 Ly~VvTyae 86 (148)
T PF09201_consen 78 LYYVVTYAE 86 (148)
T ss_dssp EEEEEEESS
T ss_pred EEEEEEecc
Confidence 999887765
No 30
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=35.85 E-value=33 Score=18.05 Aligned_cols=17 Identities=24% Similarity=0.284 Sum_probs=14.4
Q ss_pred hHHHHHHHHHHHHhCcE
Q 031317 106 NFHKAYYILDEILIAGE 122 (161)
Q Consensus 106 Nf~~vy~lLDEmid~G~ 122 (161)
+++.+..++++|...|.
T Consensus 16 ~~~~a~~~~~~M~~~gv 32 (34)
T PF13812_consen 16 DPDAALQLFDEMKEQGV 32 (34)
T ss_pred CHHHHHHHHHHHHHhCC
Confidence 47779999999998884
No 31
>cd05165 PI3Kc_I Phosphoinositide 3-kinase (PI3K), class I, catalytic domain; The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class I PI3Ks are the only enzymes capable of converting PtdIns(4,5)P2 to the critical second messenger PtdIns(3,4,5)P3. In vitro, they can also phosphorylate the substrates P
Probab=35.15 E-value=76 Score=27.89 Aligned_cols=90 Identities=12% Similarity=0.129 Sum_probs=57.0
Q ss_pred ccceEEeCCeEEEEEEeCcEEEEEEecCC-CCHHHHHHHHHHHHHHHH-----------HHhcccchh---hHHhhHHHH
Q 031317 46 LCNFVEWRGYKVVYKRYASLYFCMCVDQE-DNELEILEIIHHYVEILD-----------RYFGSVCEL---DLIFNFHKA 110 (161)
Q Consensus 46 ~~~i~~~~~~~~vy~~~~~L~f~~v~~~n-eNel~i~efL~~~ve~L~-----------~yfg~v~E~---~i~~Nf~~v 110 (161)
..|+...+.-.++|+=++-++=-.-.... ..|..=+-+=+-+++++. ..|...|+. .++.|-..+
T Consensus 221 ~~NILi~~~G~l~HIDFG~ilg~~~~~~~i~~E~~PFkLT~emv~~mg~~~~~~~s~~f~~F~~~c~~a~~~LR~~~~~i 300 (366)
T cd05165 221 NDNIMVKETGQLFHIDFGHILGNYKSKFGINRERVPFVLTPDFVHVIGRGKKDNTSEHFQRFQDLCEKAYLALRRHGNLL 300 (366)
T ss_pred CcceEEcCCCCEEEEehHHhhccCCccCCCCCCCCCeeecHHHHHHhcccCCcCCChhhhHHHHHHHHHHHHHHhCHHHH
Confidence 46677667788888888765411111111 012222334456666664 477777774 688999999
Q ss_pred HHHHHHHHhCcEeeecCHHHHHHHHH
Q 031317 111 YYILDEILIAGELQESSKKTVARLIA 136 (161)
Q Consensus 111 y~lLDEmid~G~~~eT~~~~i~~~i~ 136 (161)
.-++.=|++.|.|.-+..+. ..++.
T Consensus 301 l~l~~lM~~s~ip~~~~~~~-i~~lr 325 (366)
T cd05165 301 IILFSMMLMSGLPELTSKED-IEYLR 325 (366)
T ss_pred HHHHHHHhcCCCcccCchhH-HHHHH
Confidence 99998888999999885542 34444
No 32
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=34.22 E-value=75 Score=21.84 Aligned_cols=39 Identities=15% Similarity=-0.010 Sum_probs=22.0
Q ss_pred HHHHHHHHHhcccchhhHHhhHHHHHHHHHHHHhCcEee
Q 031317 86 HYVEILDRYFGSVCELDLIFNFHKAYYILDEILIAGELQ 124 (161)
Q Consensus 86 ~~ve~L~~yfg~v~E~~i~~Nf~~vy~lLDEmid~G~~~ 124 (161)
++-..+...+++..+.+.-..-.....+++.|.|.|++-
T Consensus 3 kIL~~l~~~~~~~~~~~~~~~~~~~~~il~~L~d~GyI~ 41 (88)
T PF09639_consen 3 KILKYLYKCMKNGKEPDPDITDSYWSDILRMLQDEGYIK 41 (88)
T ss_dssp HHHHHHHHH-S---HHHHTS-HHHHHHHHHHHHHHTSEE
T ss_pred hHHHHHHHHHcCCCCCCcchhHHHHHHHHHHHHHCCCcc
Confidence 333444445555544433222377888999999999994
No 33
>cd08324 CARD_NOD1_CARD4 Caspase activation and recruitment domain similar to that found in NOD1. Caspase activation and recruitment domain (CARD) found in human NOD1 (CARD4) and similar proteins. NOD1 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD1, as well as NOD2, the N-terminal effector domain is a CARD. Nod1-CARD has been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form hom
Probab=32.88 E-value=40 Score=23.62 Aligned_cols=44 Identities=11% Similarity=0.159 Sum_probs=35.2
Q ss_pred hhhHHhhHHHHHHHHHHHHhCcEeeecCHHHHHHHHHhhhhhHH
Q 031317 100 ELDLIFNFHKAYYILDEILIAGELQESSKKTVARLIAAQDSLVE 143 (161)
Q Consensus 100 E~~i~~Nf~~vy~lLDEmid~G~~~eT~~~~i~~~i~~~~~~~~ 143 (161)
-..++.+..-|-=+||.+.++|++.+-+-+.+...=+.++++.+
T Consensus 7 Re~LV~rI~~v~plLD~Ll~n~~it~E~y~~V~a~~T~qdkmRk 50 (85)
T cd08324 7 RELLVTHIRNTQCLVDNLLKNDYFSTEDAEIVCACPTQPDKVRK 50 (85)
T ss_pred HHHHHHHHHhhHHHHHHHhccCCccHHHHHHHHhCCCCHHHHHH
Confidence 34677888888899999999999999888877776666666653
No 34
>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=32.17 E-value=42 Score=17.30 Aligned_cols=19 Identities=21% Similarity=0.260 Sum_probs=15.7
Q ss_pred hHHHHHHHHHHHHhCcEee
Q 031317 106 NFHKAYYILDEILIAGELQ 124 (161)
Q Consensus 106 Nf~~vy~lLDEmid~G~~~ 124 (161)
+++.+..++++|...|...
T Consensus 15 ~~~~a~~~~~~M~~~g~~p 33 (35)
T TIGR00756 15 RVEEALELFKEMLERGIEP 33 (35)
T ss_pred CHHHHHHHHHHHHHcCCCC
Confidence 4778899999999988754
No 35
>PRK13190 putative peroxiredoxin; Provisional
Probab=31.27 E-value=1e+02 Score=24.23 Aligned_cols=21 Identities=24% Similarity=0.401 Sum_probs=18.0
Q ss_pred eEEEEEEcCCCCeEEEecCCC
Q 031317 2 IHFVLLISRQGKVRLTKWYSP 22 (161)
Q Consensus 2 I~al~Iln~~G~~~l~K~Y~~ 22 (161)
+.+.||+|.+|+++....|..
T Consensus 117 ~p~~fiId~~G~I~~~~~~~~ 137 (202)
T PRK13190 117 VRGVFIIDPNQIVRWMIYYPA 137 (202)
T ss_pred EeEEEEECCCCEEEEEEEeCC
Confidence 468899999999998887765
No 36
>PF04614 Pex19: Pex19 protein family; InterPro: IPR006708 Peroxisome(s) form an intracellular compartment, bounded by a typical lipid bilayer membrane. Peroxisome functions are often specialised by organism and cell type; two widely distributed and well-conserved functions are H2O2-based respiration and fatty acid beta-oxidation. Other functions include ether lipid (plasmalogen) synthesis and cholesterol synthesis in animals, the glyoxylate cycle in germinating seeds ("glyoxysomes"), photorespiration in leaves, glycolysis in trypanosomes ("glycosomes"), and methanol and/or amine oxidation and assimilation in some yeasts. PEX genes encode the machinery ("peroxins") required to assemble the peroxisome. Membrane assembly and maintenance requires three of these (peroxins 3, 16, and 19) and may occur without the import of the matrix (lumen) enzymes. Matrix protein import follows a branched pathway of soluble recycling receptors, with one branch for each class of peroxisome targeting sequence (two are well characterised), and a common trunk for all. At least one of these receptors, Pex5p, enters and exits peroxisomes as it functions. Proliferation of the organelle is regulated by Pex11p. Peroxisome biogenesis is remarkably conserved among eukaryotes. A group of fatal, inherited neuropathologies are recognised as peroxisome biogenesis diseases. ; GO: 0005777 peroxisome; PDB: 2WL8_B 2W85_B.
Probab=29.89 E-value=1.2e+02 Score=25.09 Aligned_cols=21 Identities=14% Similarity=0.056 Sum_probs=11.7
Q ss_pred HhhHHHHHHHHHHHHhCcEee
Q 031317 104 IFNFHKAYYILDEILIAGELQ 124 (161)
Q Consensus 104 ~~Nf~~vy~lLDEmid~G~~~ 124 (161)
..+|..|..+++||=+.|.|-
T Consensus 195 ~~~~~~i~~lmqemQ~~G~PP 215 (248)
T PF04614_consen 195 PERREKIMELMQEMQELGQPP 215 (248)
T ss_dssp HHHHHHHHHHHHHHHHT----
T ss_pred HHHHHHHHHHHHHHHHcCCCc
Confidence 456677777777777777664
No 37
>cd00896 PI3Kc_III Phosphoinositide 3-kinase (PI3K), class III, catalytic domain; The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class III PI3Ks, also called Vps34 (vacuolar protein sorting 34), contain an N-terminal lipid binding C2 domain, a PI3K homology domain of unknown function, and a C-termin
Probab=29.44 E-value=1.1e+02 Score=26.70 Aligned_cols=89 Identities=11% Similarity=0.024 Sum_probs=57.9
Q ss_pred ccceEEeCCeEEEEEEeCcEEEEEEecCCCCHHHHHHHHHHHHHHHHH-------Hhcccchh---hHHhhHHHHHHHHH
Q 031317 46 LCNFVEWRGYKVVYKRYASLYFCMCVDQEDNELEILEIIHHYVEILDR-------YFGSVCEL---DLIFNFHKAYYILD 115 (161)
Q Consensus 46 ~~~i~~~~~~~~vy~~~~~L~f~~v~~~neNel~i~efL~~~ve~L~~-------yfg~v~E~---~i~~Nf~~vy~lLD 115 (161)
..|++...+-.++|+=++-++ .-....+. .=+-+-+-++++|.- .|...|+. .++.|...+..++.
T Consensus 211 ~~NILi~~~G~~~HIDFG~il--g~~p~~~~--~PFrLT~~mv~~mGg~~s~~~~~F~~~c~~~~~~lR~~~~~il~l~~ 286 (350)
T cd00896 211 LDNLLLTKDGKLFHIDFGYIL--GRDPKPFP--PPMKLCKEMVEAMGGAQSEGYQEFKSYCCEAYNILRKSANLILNLFS 286 (350)
T ss_pred CCcEEEcCCCCEEEEEhHHhh--CCCCCCCC--CCeeccHHHHHHhCCCCCcchHHHHHHHHHHHHHHHhCHHHHHHHHH
Confidence 466776677888888887544 11111111 222233455666643 67777774 68899999999999
Q ss_pred HHHhCcEeeec-CHHHHHHHHHhh
Q 031317 116 EILIAGELQES-SKKTVARLIAAQ 138 (161)
Q Consensus 116 Emid~G~~~eT-~~~~i~~~i~~~ 138 (161)
=|++.|.|.-+ +++..+.++...
T Consensus 287 lm~~~~ip~~~~~~~~~i~~l~~r 310 (350)
T cd00896 287 LMVDANIPDIALDPDKAILKVQEK 310 (350)
T ss_pred HHcCCCCcccccCHHHHHHHHHHH
Confidence 99999999754 566566666543
No 38
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=28.34 E-value=58 Score=22.54 Aligned_cols=23 Identities=13% Similarity=0.105 Sum_probs=19.3
Q ss_pred hhHHHHHHHHHHHHhCcEeeecC
Q 031317 105 FNFHKAYYILDEILIAGELQESS 127 (161)
Q Consensus 105 ~Nf~~vy~lLDEmid~G~~~eT~ 127 (161)
.+-..|...+|++++.|.+..|-
T Consensus 77 ~~~~~v~~al~~L~~eG~IYsTi 99 (102)
T PF08784_consen 77 MSENEVRKALDFLSNEGHIYSTI 99 (102)
T ss_dssp S-HHHHHHHHHHHHHTTSEEESS
T ss_pred cCHHHHHHHHHHHHhCCeEeccc
Confidence 44578999999999999999883
No 39
>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=28.12 E-value=1.4e+02 Score=23.38 Aligned_cols=20 Identities=30% Similarity=0.581 Sum_probs=17.1
Q ss_pred EEEEEEcCCCCeEEEecCCC
Q 031317 3 HFVLLISRQGKVRLTKWYSP 22 (161)
Q Consensus 3 ~al~Iln~~G~~~l~K~Y~~ 22 (161)
.+.||+|.+|+++....|..
T Consensus 118 r~~fiID~~G~I~~~~~~~~ 137 (203)
T cd03016 118 RAVFIIDPDKKIRLILYYPA 137 (203)
T ss_pred eEEEEECCCCeEEEEEecCC
Confidence 46899999999999888853
No 40
>COG4114 FhuF Uncharacterized Fe-S protein [General function prediction only]
Probab=27.76 E-value=1.7e+02 Score=24.41 Aligned_cols=40 Identities=20% Similarity=0.071 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHHHHHhcccchhhHHhh-HHHHHHHHHHHH
Q 031317 78 LEILEIIHHYVEILDRYFGSVCELDLIFN-FHKAYYILDEIL 118 (161)
Q Consensus 78 l~i~efL~~~ve~L~~yfg~v~E~~i~~N-f~~vy~lLDEmi 118 (161)
.++-+-|..+++.|+++ |+++-+-+=.| +..++..||||.
T Consensus 147 tL~~~hL~pv~~~Lea~-g~In~rLlWnNtgyli~wyl~e~k 187 (251)
T COG4114 147 TLISQHLVPVVQALEAT-GGINGRLLWNNTGYLINWYLTEMK 187 (251)
T ss_pred HHHHHHHHHHHHHHHHh-cCCChhhhhhhhHHHHHHHHHHHH
Confidence 45556677788888877 66777777788 889999999998
No 41
>PF03259 Robl_LC7: Roadblock/LC7 domain; InterPro: IPR004942 This family includes proteins that are about 100 amino acids long and have been shown to be related []. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions []. This family also includes Golgi-associated MP1 adapter protein (Q9Y2Q5 from SWISSPROT) and MglB from Myxococcus xanthus (Q50883 from SWISSPROT), a protein involved in gliding motility []. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role.; PDB: 2B95_B 1Z09_A 2E8J_B 2HZ5_B 3KYE_A 2ZL1_B 1SKO_B 3CPT_B 1VEU_B 1VET_B ....
Probab=27.70 E-value=1.8e+02 Score=18.90 Aligned_cols=68 Identities=9% Similarity=0.067 Sum_probs=34.3
Q ss_pred eEEEEEEcCCCCeEEEecCCCCCHHHHHHHHHHHHHHHhc-----cCCC-ccceEEeCCeEEEEEEeCcEEEEE
Q 031317 2 IHFVLLISRQGKVRLTKWYSPYTQKERSKVIRELSGVILT-----RGPK-LCNFVEWRGYKVVYKRYASLYFCM 69 (161)
Q Consensus 2 I~al~Iln~~G~~~l~K~Y~~~~~~~~~~~~~~i~~~i~~-----r~~~-~~~i~~~~~~~~vy~~~~~L~f~~ 69 (161)
+++.+++|++|.++-+....+.....-.+....++..... ..+. ..-++..++..++-....+=++++
T Consensus 15 v~~~~l~~~dG~~i~~~~~~~~~~~~~aa~~a~~~~~~~~~~~~l~~~~~~~v~i~~~~~~i~i~~~~~~~~L~ 88 (91)
T PF03259_consen 15 VRGAVLVDKDGLVIASSGIDDDDAEKLAAMAASLLAAAEKLAKELGEGELEQVRIETEKGEIIITPVGDFYLLV 88 (91)
T ss_dssp EEEEEEEETTSEEEEETSSSHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEEEEEESSEEEEEEECSTCEEEE
T ss_pred eeEEEEEcCCCCEEEEecCCcccHHHHHHHHHHHHHHHHHHHHHhCCCCcEEEEEEECCCEEEEEEcCCCEEEE
Confidence 5788999999999988222111111112223333322111 1111 233555677777766666634333
No 42
>PF13041 PPR_2: PPR repeat family
Probab=26.66 E-value=50 Score=19.45 Aligned_cols=22 Identities=23% Similarity=0.268 Sum_probs=18.4
Q ss_pred hhHHHHHHHHHHHHhCcEeeec
Q 031317 105 FNFHKAYYILDEILIAGELQES 126 (161)
Q Consensus 105 ~Nf~~vy~lLDEmid~G~~~eT 126 (161)
.+++.+..+++||...|.....
T Consensus 17 ~~~~~a~~l~~~M~~~g~~P~~ 38 (50)
T PF13041_consen 17 GKFEEALKLFKEMKKRGIKPDS 38 (50)
T ss_pred cCHHHHHHHHHHHHHcCCCCCH
Confidence 4688999999999999986544
No 43
>PF14903 WG_beta_rep: WG containing repeat
Probab=26.56 E-value=66 Score=17.32 Aligned_cols=17 Identities=24% Similarity=0.485 Sum_probs=14.3
Q ss_pred EEcCCCCeEEEecCCCC
Q 031317 7 LISRQGKVRLTKWYSPY 23 (161)
Q Consensus 7 Iln~~G~~~l~K~Y~~~ 23 (161)
++|.+|++++.--|+..
T Consensus 3 ~id~~G~~vi~~~yd~i 19 (35)
T PF14903_consen 3 YIDKNGKIVIPPKYDEI 19 (35)
T ss_pred EEeCCCCEEEEccccCc
Confidence 68999999998888763
No 44
>cd05168 PI4Kc_III_beta Phosphoinositide 4-kinase (PI4K), Type III, beta isoform, catalytic domain; The PI4K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. PI4Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 4-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) to generate PtdIns(4)P, the major precursor in the synthesis of other phosphoinositides including PtdIns(4,5)P2, PtdIns(3,4)P2, and PtdIns(3,4,5)P3. Two isoforms of type III PI4K, alpha and beta, exist in most eukaryotes. PI4KIIIbeta (also called Pik1p in yeast) is a 110 kDa protein that is localized to the Golgi and the nucleus. It is required for maintaining the structural integrity of the Golgi complex (GC), and is a key regulator of protein transport from the GC to the plasma membrane. PI4KII
Probab=26.49 E-value=1.2e+02 Score=25.74 Aligned_cols=80 Identities=9% Similarity=0.053 Sum_probs=49.7
Q ss_pred ccceEEeCCeEEEEEEeCcEEEEEEecCCCCHHHHHHHHHHHHHHHH-------HHhcccchh---hHHhhHHHHHHHHH
Q 031317 46 LCNFVEWRGYKVVYKRYASLYFCMCVDQEDNELEILEIIHHYVEILD-------RYFGSVCEL---DLIFNFHKAYYILD 115 (161)
Q Consensus 46 ~~~i~~~~~~~~vy~~~~~L~f~~v~~~neNel~i~efL~~~ve~L~-------~yfg~v~E~---~i~~Nf~~vy~lLD 115 (161)
..|++..++-.++|+=++.++=.+-.. -.-|..=+-+=..++++|. ..|...|+. .++.|-..+..+++
T Consensus 150 ~~NILi~~~G~liHIDFG~~fg~~~~~-~~~E~vPFrLT~~mv~~mGg~~s~~~~~F~~~c~~~~~~LR~~~~~il~ll~ 228 (293)
T cd05168 150 NGNILIDNDGHIIHIDFGFMLSNSPGN-VGFETAPFKLTQEYIEVMGGVNSDLFNYFKKLFLKGFMALRKHVDRIILLVE 228 (293)
T ss_pred CCceEEcCCCCEEEEehHHhhcccccC-CCCCCCCEEecHHHHHHhCCCCCchhHHHHHHHHHHHHHHHhchHHHHHHHH
Confidence 356766667778888876444221111 0011112223344555554 366667775 58999999999999
Q ss_pred HHHhC-cEeeec
Q 031317 116 EILIA-GELQES 126 (161)
Q Consensus 116 Emid~-G~~~eT 126 (161)
=|+.. |.|.-+
T Consensus 229 ~m~~~~~lp~f~ 240 (293)
T cd05168 229 IMQSDSKLPCFK 240 (293)
T ss_pred HHccCCCCcccc
Confidence 99987 999977
No 45
>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=26.06 E-value=1.3e+02 Score=18.88 Aligned_cols=29 Identities=17% Similarity=0.304 Sum_probs=17.5
Q ss_pred HHHHHHHHHhCcEeeecCHHHHHHHHHhhhhh
Q 031317 110 AYYILDEILIAGELQESSKKTVARLIAAQDSL 141 (161)
Q Consensus 110 vy~lLDEmid~G~~~eT~~~~i~~~i~~~~~~ 141 (161)
.-+.||||+..|.+. |+...+=+...|+.
T Consensus 15 L~dtLDeli~~~~I~---p~La~kVL~~FDks 43 (49)
T PF02268_consen 15 LTDTLDELIQEGKIT---PQLAMKVLEQFDKS 43 (49)
T ss_dssp HHHHHHHHHHTTSS----HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCC---HHHHHHHHHHHHHH
Confidence 346789999998874 55333334445544
No 46
>smart00571 DDT domain in different transcription and chromosome remodeling factors.
Probab=25.60 E-value=59 Score=20.95 Aligned_cols=17 Identities=18% Similarity=0.442 Sum_probs=14.8
Q ss_pred CHHHHHHHHHHHHHHHH
Q 031317 76 NELEILEIIHHYVEILD 92 (161)
Q Consensus 76 Nel~i~efL~~~ve~L~ 92 (161)
+-++++|||+.|-++|.
T Consensus 6 d~l~V~eFl~~F~~~L~ 22 (63)
T smart00571 6 DLLMVYEFLRSFGKVLG 22 (63)
T ss_pred HHHHHHHHHHHHHHHhC
Confidence 56899999999999983
No 47
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=23.84 E-value=1.4e+02 Score=19.71 Aligned_cols=31 Identities=23% Similarity=0.322 Sum_probs=20.2
Q ss_pred hHHHHHHHHHHHHhCcEeeecCHHHHHHHHH
Q 031317 106 NFHKAYYILDEILIAGELQESSKKTVARLIA 136 (161)
Q Consensus 106 Nf~~vy~lLDEmid~G~~~eT~~~~i~~~i~ 136 (161)
+|..++..+++++..|++...=...+...+.
T Consensus 19 ~~~~~~~~~~~l~~~G~s~~~Il~~l~~~l~ 49 (89)
T PF08542_consen 19 DFKEARKKLYELLVEGYSASDILKQLHEVLV 49 (89)
T ss_dssp CHHHHHHHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 8899999999999889976543333333333
No 48
>COG0450 AhpC Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=23.37 E-value=1.9e+02 Score=23.26 Aligned_cols=21 Identities=14% Similarity=0.156 Sum_probs=19.0
Q ss_pred eEEEEEEcCCCCeEEEecCCC
Q 031317 2 IHFVLLISRQGKVRLTKWYSP 22 (161)
Q Consensus 2 I~al~Iln~~G~~~l~K~Y~~ 22 (161)
..++||+|.+|.+|..=+|..
T Consensus 124 ~R~~FIIDp~g~ir~~~v~~~ 144 (194)
T COG0450 124 LRGTFIIDPDGVIRHILVNPL 144 (194)
T ss_pred eeEEEEECCCCeEEEEEEecC
Confidence 468999999999999999976
No 49
>cd00893 PI4Kc_III Phosphoinositide 4-kinase (PI4K), Type III, catalytic domain; The PI4K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. PI4Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 4-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) to generate PtdIns(4)P, the major precursor in the synthesis of other phosphoinositides including PtdIns(4,5)P2, PtdIns(3,4)P2, and PtdIns(3,4,5)P3. There are two types of PI4Ks, types II and III. Type II PI4Ks lack the characteristic catalytic kinase domain present in PI3Ks and type III PI4Ks, and are excluded from this family. Two isoforms of type III PI4K, alpha and beta, exist in most eukaryotes.
Probab=23.01 E-value=1.2e+02 Score=25.69 Aligned_cols=80 Identities=8% Similarity=0.024 Sum_probs=51.3
Q ss_pred ccceEEeCCeEEEEEEeCcEEEEEEecCCC-CHHHHHHHHHHHHHHHH-------HHhcccchh---hHHhhHHHHHHHH
Q 031317 46 LCNFVEWRGYKVVYKRYASLYFCMCVDQED-NELEILEIIHHYVEILD-------RYFGSVCEL---DLIFNFHKAYYIL 114 (161)
Q Consensus 46 ~~~i~~~~~~~~vy~~~~~L~f~~v~~~ne-Nel~i~efL~~~ve~L~-------~yfg~v~E~---~i~~Nf~~vy~lL 114 (161)
..|++..+.-.++|+=++-++=..-.. +- .|..=+-+=.-++++|. .+|..+|+. .++.|-+.+..++
T Consensus 148 ~~NILid~~G~liHIDFG~ilg~~p~~-~~~~E~~PFrLT~emv~~mGg~~s~~f~~F~~~c~~~~~~lR~~~~~il~ll 226 (289)
T cd00893 148 NGNILLDSDGHIIHIDFGFILDSSPGN-NLGFEPAAFKFTKEMVDFMGGKKSDDFKKFRYLCLRGFIAVRKHMDLVISLV 226 (289)
T ss_pred CCceEECCCCCEEEEehHHhhCcCCcC-CCCCCCCCeeecHHHHHHhCCCCChhHHHHHHHHHHHHHHHhhCHHHHHHHH
Confidence 356776677788888876443221111 00 11222333345555553 357777774 6889999999999
Q ss_pred HHHHhCcEeeec
Q 031317 115 DEILIAGELQES 126 (161)
Q Consensus 115 DEmid~G~~~eT 126 (161)
.=|++.|+|.-+
T Consensus 227 ~~m~~~~lp~~~ 238 (289)
T cd00893 227 YLLIFSGLPCFR 238 (289)
T ss_pred HHHccCCCcccC
Confidence 999999999887
No 50
>PRK13191 putative peroxiredoxin; Provisional
Probab=22.85 E-value=1.8e+02 Score=23.16 Aligned_cols=21 Identities=29% Similarity=0.641 Sum_probs=18.0
Q ss_pred eEEEEEEcCCCCeEEEecCCC
Q 031317 2 IHFVLLISRQGKVRLTKWYSP 22 (161)
Q Consensus 2 I~al~Iln~~G~~~l~K~Y~~ 22 (161)
..+.||+|.+|.++..-+|..
T Consensus 124 ~r~tfIID~~G~Ir~~~~~~~ 144 (215)
T PRK13191 124 VRAVFIVDDKGTVRLILYYPM 144 (215)
T ss_pred eEEEEEECCCCEEEEEEecCC
Confidence 467899999999999988864
No 51
>PF02791 DDT: DDT domain; InterPro: IPR004022 This domain is predicted to be a DNA binding domain. The DDT domain is named after (DNA binding homeobox and Different Transcription factors). It is found in foetal Alzheimer antigen and several hypothetical and uncharacterised proteins.
Probab=22.77 E-value=79 Score=20.11 Aligned_cols=18 Identities=22% Similarity=0.418 Sum_probs=15.1
Q ss_pred CHHHHHHHHHHHHHHHHH
Q 031317 76 NELEILEIIHHYVEILDR 93 (161)
Q Consensus 76 Nel~i~efL~~~ve~L~~ 93 (161)
+-+++++||+.+-++|.-
T Consensus 6 ~~L~v~~Fl~~F~~~L~L 23 (61)
T PF02791_consen 6 DLLMVWEFLNTFGEVLGL 23 (61)
T ss_pred HHHHHHHHHHHHHHHHcC
Confidence 458899999999998873
No 52
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=22.01 E-value=1.1e+02 Score=21.04 Aligned_cols=41 Identities=15% Similarity=0.169 Sum_probs=33.9
Q ss_pred cccchhhHHhhHH----HHHHHHHHHHhCcEeeecCHHHHHHHHHh
Q 031317 96 GSVCELDLIFNFH----KAYYILDEILIAGELQESSKKTVARLIAA 137 (161)
Q Consensus 96 g~v~E~~i~~Nf~----~vy~lLDEmid~G~~~eT~~~~i~~~i~~ 137 (161)
++..|..|.+-|. ..|+.|+-++|.--++..+|. +++++..
T Consensus 21 ~GaKe~aIre~fGls~~rYyq~Ln~LiD~p~Ala~~P~-lv~RLRR 65 (77)
T PF11662_consen 21 GGAKEEAIREEFGLSPTRYYQRLNALIDDPAALAADPV-LVRRLRR 65 (77)
T ss_pred CCCcHHHHHHHHCCCHHHHHHHHHHHhCChHHHHhCcH-HHHHHHH
Confidence 4568888887664 789999999999999999998 6666664
No 53
>KOG1766 consensus Enhancer of rudimentary [General function prediction only]
Probab=21.98 E-value=1.6e+02 Score=21.19 Aligned_cols=42 Identities=5% Similarity=0.218 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHhccc--chhhHHhhHHHHHHHHHHHHhCc
Q 031317 80 ILEIIHHYVEILDRYFGSV--CELDLIFNFHKAYYILDEILIAG 121 (161)
Q Consensus 80 i~efL~~~ve~L~~yfg~v--~E~~i~~Nf~~vy~lLDEmid~G 121 (161)
+-|.+..+..+.+++++.. +-..|-+....+|+.+|.+.|--
T Consensus 25 v~e~megiCk~yEe~Lkk~nPs~~~ITYDIsqlfeFiD~L~DlS 68 (104)
T KOG1766|consen 25 VTECMEGICKMYEEHLKKKNPSAPPITYDISQLFEFIDDLADLS 68 (104)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCcceeHHHHHHHHHHHhhhh
Confidence 5567788888999999765 55678889999999999988743
No 54
>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=21.48 E-value=1.6e+02 Score=21.86 Aligned_cols=34 Identities=24% Similarity=0.285 Sum_probs=22.8
Q ss_pred HHHHHHHHhcccchhhHHhhHHHHHHHHHHHHhCcEe
Q 031317 87 YVEILDRYFGSVCELDLIFNFHKAYYILDEILIAGEL 123 (161)
Q Consensus 87 ~ve~L~~yfg~v~E~~i~~Nf~~vy~lLDEmid~G~~ 123 (161)
+.+.|..=|.++. -.=|-..||-.|+|+++.|+.
T Consensus 37 ~Ld~lr~EFk~~G---y~P~hsEvYraLHeL~~dGil 70 (122)
T PF02334_consen 37 LLDELRSEFKPLG---YRPNHSEVYRALHELVDDGIL 70 (122)
T ss_dssp HHHHHHHHHTTTT-------HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHhhhcC---CCCCHHHHHHHHHHHHhhhHH
Confidence 3455666565543 556778999999999999997
No 55
>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=20.83 E-value=1e+02 Score=22.49 Aligned_cols=19 Identities=26% Similarity=0.333 Sum_probs=15.7
Q ss_pred EEEEEcCCCCeEEEecCCC
Q 031317 4 FVLLISRQGKVRLTKWYSP 22 (161)
Q Consensus 4 al~Iln~~G~~~l~K~Y~~ 22 (161)
+++|+|.+|+++|.|.++.
T Consensus 7 ~~ii~~~~~~vLL~~r~~~ 25 (147)
T cd03671 7 GVVLFNEDGKVFVGRRIDT 25 (147)
T ss_pred EEEEEeCCCEEEEEEEcCC
Confidence 5788899999999887653
No 56
>PRK15000 peroxidase; Provisional
Probab=20.78 E-value=2.1e+02 Score=22.42 Aligned_cols=21 Identities=24% Similarity=0.177 Sum_probs=17.3
Q ss_pred eEEEEEEcCCCCeEEEecCCC
Q 031317 2 IHFVLLISRQGKVRLTKWYSP 22 (161)
Q Consensus 2 I~al~Iln~~G~~~l~K~Y~~ 22 (161)
+.+.||+|.+|+++....+..
T Consensus 125 ~r~tfiID~~G~I~~~~~~~~ 145 (200)
T PRK15000 125 LRGSFLIDANGIVRHQVVNDL 145 (200)
T ss_pred EeEEEEECCCCEEEEEEecCC
Confidence 468899999999999877643
No 57
>PRK13599 putative peroxiredoxin; Provisional
Probab=20.49 E-value=2e+02 Score=22.93 Aligned_cols=21 Identities=24% Similarity=0.683 Sum_probs=17.6
Q ss_pred eEEEEEEcCCCCeEEEecCCC
Q 031317 2 IHFVLLISRQGKVRLTKWYSP 22 (161)
Q Consensus 2 I~al~Iln~~G~~~l~K~Y~~ 22 (161)
+.++||+|.+|+++..-+|..
T Consensus 119 ~R~tfIID~dG~Ir~~~~~p~ 139 (215)
T PRK13599 119 VRAVFIVDDKGTIRLIMYYPQ 139 (215)
T ss_pred eeEEEEECCCCEEEEEEEcCC
Confidence 468899999999999976653
No 58
>cd00894 PI3Kc_IB_gamma Phosphoinositide 3-kinase (PI3K), class IB, gamma isoform, catalytic domain; The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. PI3Ks can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class I PI3Ks are the only enzymes capable of converting PtdIns(4,5)P2 to the critical second messenger PtdIns(3,4,5)P3. Class I enzymes are heterodimers and exist in multiple isoforms consisting of one catalytic subunit (out of four isoforms) and one of several regulatory subunits. They are further classified into class IA (alpha, beta and
Probab=20.16 E-value=2e+02 Score=25.31 Aligned_cols=82 Identities=13% Similarity=0.150 Sum_probs=50.4
Q ss_pred ccceEEeCCeEEEEEEeCcEEEEEEecC--C-CCHHHHHHHHHHHHHHHH----------HHhcccchh---hHHhhHHH
Q 031317 46 LCNFVEWRGYKVVYKRYASLYFCMCVDQ--E-DNELEILEIIHHYVEILD----------RYFGSVCEL---DLIFNFHK 109 (161)
Q Consensus 46 ~~~i~~~~~~~~vy~~~~~L~f~~v~~~--n-eNel~i~efL~~~ve~L~----------~yfg~v~E~---~i~~Nf~~ 109 (161)
..|+...+.-.++|+=++-++ .-... + ..|..=+-+=.-+++++. ..|...|+. .++.|-..
T Consensus 221 ndNImi~~~G~lfHIDFG~il--g~~~~~~gi~~E~~PFkLT~e~v~vmg~~gg~~s~~f~~F~~~c~~a~~~LRk~~~l 298 (365)
T cd00894 221 NDNIMITETGNLFHIDFGHIL--GNYKSFLGINKERVPFVLTPDFLFVMGTSGKKTSLHFQKFQDVCVKAYLALRHHTNL 298 (365)
T ss_pred ccceeEcCCCCEEEEeeHHhh--CCCCccCCCCCCCCCeeecHHHHHHhCccCCcCChhHHHHHHHHHHHHHHHHhhHHH
Confidence 356666666677888776444 11110 0 011222223355566664 356676664 68899999
Q ss_pred HHHHHHHHHhCcEeeecCHH
Q 031317 110 AYYILDEILIAGELQESSKK 129 (161)
Q Consensus 110 vy~lLDEmid~G~~~eT~~~ 129 (161)
+.-++.=|++.|+|.-+..+
T Consensus 299 il~L~~lM~~sgip~l~~~~ 318 (365)
T cd00894 299 LIILFSMMLMTGMPQLTSKE 318 (365)
T ss_pred HHHHHHHHhcCCCcccCcch
Confidence 99999888899999877544
Done!