Query 032349
Match_columns 142
No_of_seqs 113 out of 838
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 12:56:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032349.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032349hhsearch_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 3.3E-43 7.3E-48 251.8 18.9 141 1-141 1-141 (141)
2 COG5030 APS2 Clathrin adaptor 100.0 1.5E-41 3.3E-46 237.7 14.1 141 1-141 1-141 (152)
3 KOG0936 Clathrin adaptor compl 100.0 6.8E-38 1.5E-42 222.5 14.2 141 1-141 1-147 (182)
4 KOG0934 Clathrin adaptor compl 100.0 2.8E-38 6E-43 220.8 7.6 140 1-140 1-140 (145)
5 KOG0935 Clathrin adaptor compl 100.0 1.9E-37 4.2E-42 212.4 11.6 142 1-142 1-143 (143)
6 KOG3343 Vesicle coat complex C 100.0 2.1E-31 4.5E-36 190.5 12.7 134 2-138 9-146 (175)
7 KOG0938 Adaptor complexes medi 100.0 9.6E-30 2.1E-34 201.1 12.5 134 1-138 1-135 (446)
8 KOG2740 Clathrin-associated pr 99.9 4E-23 8.7E-28 164.5 9.3 134 1-136 1-136 (418)
9 KOG0937 Adaptor complexes medi 99.9 1.2E-21 2.5E-26 159.6 13.7 134 2-138 1-136 (424)
10 COG5541 RET3 Vesicle coat comp 99.9 2.7E-21 5.8E-26 138.3 9.8 133 2-137 8-152 (187)
11 KOG2635 Medium subunit of clat 99.2 1.4E-10 3E-15 95.2 12.0 134 2-137 3-136 (512)
12 PF15001 AP-5_subunit_s1: AP-5 97.5 0.013 2.8E-07 44.0 14.7 79 54-132 103-182 (189)
13 PF03164 Mon1: Trafficking pro 96.5 0.068 1.5E-06 44.7 12.2 86 3-92 12-100 (415)
14 PF08923 MAPKK1_Int: Mitogen-a 95.0 0.75 1.6E-05 32.0 10.9 92 2-93 17-114 (119)
15 PF04099 Sybindin: Sybindin-li 94.1 1.3 2.8E-05 31.6 10.2 93 2-95 1-115 (142)
16 KOG0862 Synaptobrevin/VAMP-lik 92.9 3.3 7.2E-05 31.7 11.2 71 26-97 31-101 (216)
17 PF13774 Longin: Regulated-SNA 92.2 1.7 3.8E-05 27.6 7.8 49 48-96 17-65 (83)
18 KOG0997 Uncharacterized conser 88.0 7 0.00015 33.6 9.7 80 4-84 119-198 (523)
19 KOG0859 Synaptobrevin/VAMP-lik 87.8 10 0.00023 28.8 11.1 87 7-97 6-93 (217)
20 KOG0781 Signal recognition par 85.8 23 0.00049 30.8 11.6 112 1-116 1-116 (587)
21 COG5122 TRS23 Transport protei 82.5 14 0.0003 25.7 9.2 91 2-95 3-106 (134)
22 PF04086 SRP-alpha_N: Signal r 65.4 63 0.0014 25.2 9.2 50 48-97 20-71 (279)
23 PF08006 DUF1700: Protein of u 65.3 20 0.00042 26.2 5.2 50 87-136 6-61 (181)
24 COG3322 Predicted periplasmic 59.5 8.7 0.00019 30.9 2.6 23 2-24 104-126 (295)
25 PF09201 SRX: SRX; InterPro: 59.0 65 0.0014 23.2 6.8 71 1-73 1-86 (148)
26 PF05228 CHASE4: CHASE4 domain 52.0 55 0.0012 22.7 5.6 21 2-22 50-72 (161)
27 PF02334 RTP: Replication term 52.0 27 0.00059 24.2 3.7 33 88-123 38-70 (122)
28 PF01535 PPR: PPR repeat; Int 47.8 18 0.00039 17.5 1.9 18 105-122 14-31 (31)
29 KOG3368 Transport protein part 45.1 1.1E+02 0.0024 21.8 10.8 85 2-89 3-102 (140)
30 PF13812 PPR_3: Pentatricopept 44.4 20 0.00044 17.8 1.8 17 106-122 16-32 (34)
31 PF08784 RPA_C: Replication pr 44.2 24 0.00052 23.2 2.5 29 98-126 66-98 (102)
32 PF02268 TFIIA_gamma_N: Transc 41.8 32 0.00069 20.1 2.4 15 110-124 15-29 (49)
33 KOG3369 Transport protein part 40.1 1.6E+02 0.0035 22.1 10.1 45 49-95 125-170 (199)
34 PF14903 WG_beta_rep: WG conta 39.1 32 0.0007 17.5 2.1 17 7-23 3-19 (35)
35 PF08217 DUF1712: Fungal domai 35.8 3.2E+02 0.0069 24.3 11.4 73 44-118 55-135 (604)
36 COG1049 AcnB Aconitase B [Ener 34.9 66 0.0014 28.9 4.2 40 98-140 602-641 (852)
37 cd03016 PRX_1cys Peroxiredoxin 34.6 1.2E+02 0.0027 22.3 5.3 19 3-21 118-136 (203)
38 TIGR00756 PPR pentatricopeptid 34.3 37 0.0008 16.5 1.8 19 106-124 15-33 (35)
39 PRK13190 putative peroxiredoxi 33.7 1.1E+02 0.0024 22.7 5.0 21 2-22 117-137 (202)
40 cd08324 CARD_NOD1_CARD4 Caspas 30.4 46 0.001 21.8 2.0 41 100-140 7-47 (85)
41 smart00571 DDT domain in diffe 30.1 47 0.001 20.1 2.0 16 76-91 6-21 (63)
42 PF13041 PPR_2: PPR repeat fam 29.9 41 0.00088 18.7 1.6 22 105-126 17-38 (50)
43 COG0450 AhpC Peroxiredoxin [Po 28.0 1.7E+02 0.0038 22.1 5.0 21 2-22 124-144 (194)
44 PF02791 DDT: DDT domain; Int 27.5 60 0.0013 19.4 2.1 18 76-93 6-23 (61)
45 PF09639 YjcQ: YjcQ protein; 27.0 1.1E+02 0.0024 19.7 3.5 33 92-124 9-41 (88)
46 PRK13599 putative peroxiredoxi 26.8 1.8E+02 0.0038 22.0 5.0 21 2-22 119-139 (215)
47 COG4114 FhuF Uncharacterized F 26.5 2E+02 0.0043 22.5 5.2 39 80-119 149-188 (251)
48 KOG1373 Transport protein Sec6 26.2 1E+02 0.0022 26.1 3.8 49 79-127 123-180 (476)
49 PF03259 Robl_LC7: Roadblock/L 26.2 1.6E+02 0.0036 18.0 6.6 16 2-17 15-30 (91)
50 PRK13191 putative peroxiredoxi 25.6 2E+02 0.0043 21.7 5.1 20 2-21 124-143 (215)
51 PF13867 SAP30_Sin3_bdg: Sin3 24.5 1E+02 0.0022 18.0 2.7 23 86-108 25-49 (53)
52 PRK13189 peroxiredoxin; Provis 24.0 2.2E+02 0.0047 21.5 5.1 21 2-22 126-146 (222)
53 cd08330 CARD_ASC_NALP1 Caspase 22.7 56 0.0012 20.9 1.4 40 100-139 7-46 (82)
54 cd03015 PRX_Typ2cys Peroxiredo 22.7 2.4E+02 0.0052 20.0 5.0 17 3-19 121-137 (173)
55 PF11411 DNA_ligase_IV: DNA li 22.0 25 0.00054 19.3 -0.3 17 93-109 16-32 (36)
56 PRK15000 peroxidase; Provision 21.8 2.6E+02 0.0056 20.7 5.1 20 2-21 125-144 (200)
57 PRK15117 ABC transporter perip 21.5 36 0.00077 25.8 0.3 29 12-40 74-102 (211)
58 PF07205 DUF1413: Domain of un 20.2 2.1E+02 0.0045 17.5 3.6 25 19-43 27-51 (70)
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=3.3e-43 Score=251.79 Aligned_cols=141 Identities=38% Similarity=0.616 Sum_probs=131.7
Q ss_pred CeEEEEeecCCCCeeEEecCCCCChhhHHHHHHHHHHHHhcCCCCCCceEEeCCeEEEEEEeCCEEEEEEecCCcCHHHH
Q 032349 1 MIRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRLVVNRDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNELAY 80 (142)
Q Consensus 1 MI~~i~iln~~G~~~l~k~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~~~~~~~~~~Nel~~ 80 (142)
||+|++|+|++|+++++|||++.+..+++++.+++.+.+..+++..||++.++++++||+++++|||+++++.++||+++
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 99999999999999999999988888888888888888877777779999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhccccHHHHHHhHHHHHHHHHHHHhCcEEeecCHHHHHHHHHhhhhc
Q 032349 81 LECIHLFVEILDHFFSNVCELDLVFNFHKVYLILDEFILAGELQETSKRAIIERMGELEKL 141 (142)
Q Consensus 81 le~l~~~v~~l~~~f~~v~e~~i~~nf~~v~~lLDE~id~G~~~etd~~~i~~~i~~~~~~ 141 (142)
+++|++++++|+.|||++||+++++||+.+|++||||+|+|+|+|||+++|++|++++|+.
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 9999999999999999999999999999999999999999999999999999999999874
No 2
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=100.00 E-value=1.5e-41 Score=237.69 Aligned_cols=141 Identities=54% Similarity=0.907 Sum_probs=136.8
Q ss_pred CeEEEEeecCCCCeeEEecCCCCChhhHHHHHHHHHHHHhcCCCCCCceEEeCCeEEEEEEeCCEEEEEEecCCcCHHHH
Q 032349 1 MIRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRLVVNRDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNELAY 80 (142)
Q Consensus 1 MI~~i~iln~~G~~~l~k~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~~~~~~~~~~Nel~~ 80 (142)
||++++++|++|++|+.|||.+.+.++|.++.+++++.+++|+++.|++++..+.++|||||++|||+++++.++||+++
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 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhccccHHHHHHhHHHHHHHHHHHHhCcEEeecCHHHHHHHHHhhhhc
Q 032349 81 LECIHLFVEILDHFFSNVCELDLVFNFHKVYLILDEFILAGELQETSKRAIIERMGELEKL 141 (142)
Q Consensus 81 le~l~~~v~~l~~~f~~v~e~~i~~nf~~v~~lLDE~id~G~~~etd~~~i~~~i~~~~~~ 141 (142)
++.+|.|+++|++|||+|||.++++||.++|.+||||+.+|.++||++..+++++...++.
T Consensus 81 L~lIh~FVE~lDr~FgnVCELdlIFNF~kv~~ILdE~i~gG~i~Es~~~~vl~~v~~lda~ 141 (152)
T COG5030 81 LELIHNFVEILDRFFGNVCELDLIFNFQKVYAILDEMILGGEIIESSKNEVLEHVYALDAE 141 (152)
T ss_pred HHHHHHHHHHHHHHhccceeeEeEeeHHHHHHHHHHHHhCCeeeecCHHHHHHHHHHHHhh
Confidence 9999999999999999999999999999999999999999999999999999999877654
No 3
>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=6.8e-38 Score=222.48 Aligned_cols=141 Identities=42% Similarity=0.747 Sum_probs=135.7
Q ss_pred CeEEEEeecCCCCeeEEecCCCCChhhHHHHHHHHHHHHhcCCCCCCceEEe----C--CeEEEEEEeCCEEEEEEecCC
Q 032349 1 MIRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRLVVNRDPKFTNFVEF----R--THKVIYRRYAGLFFSLCVDIT 74 (142)
Q Consensus 1 MI~~i~iln~~G~~~l~k~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~----~--~~~~vy~~~~~l~~~~~~~~~ 74 (142)
||+|++|+|++|++|+.|||++.+.++|+.+.+++|..+++|++..|+|++. | +.+++||+|+.|||+.++|++
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 9999999999999999999999999999999999999999999888998864 3 789999999999999999999
Q ss_pred cCHHHHHHHHHHHHHHHHHHhccccHHHHHHhHHHHHHHHHHHHhCcEEeecCHHHHHHHHHhhhhc
Q 032349 75 DNELAYLECIHLFVEILDHFFSNVCELDLVFNFHKVYLILDEFILAGELQETSKRAIIERMGELEKL 141 (142)
Q Consensus 75 ~Nel~~le~l~~~v~~l~~~f~~v~e~~i~~nf~~v~~lLDE~id~G~~~etd~~~i~~~i~~~~~~ 141 (142)
|+||.++++++.||++|+++|.++||.|+++|+++++.+|+|++.+|.++||+.+.|.+.+..++|+
T Consensus 81 EsEL~iLDLIQvfVEtLDkCF~nVcELDliF~~~k~h~iL~EiV~GGmVlETn~neIv~av~~~nkl 147 (182)
T KOG0936|consen 81 ESELGILDLIQVFVETLDKCFENVCELDLIFNWQKVHAILAEIVMGGMVLETNMNEIVAAVDEQNKL 147 (182)
T ss_pred cchhHHHHHHHHHHHHHHHHHHhhhhhhheeeHHHHHHHHHHHHhCCeEEeccHHHHHHHHHHhchh
Confidence 9999999999999999999999999999999999999999999999999999999999999998876
No 4
>KOG0934 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.8e-38 Score=220.83 Aligned_cols=140 Identities=52% Similarity=0.934 Sum_probs=135.5
Q ss_pred CeEEEEeecCCCCeeEEecCCCCChhhHHHHHHHHHHHHhcCCCCCCceEEeCCeEEEEEEeCCEEEEEEecCCcCHHHH
Q 032349 1 MIRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRLVVNRDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNELAY 80 (142)
Q Consensus 1 MI~~i~iln~~G~~~l~k~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~~~~~~~~~~Nel~~ 80 (142)
||++++++|++|+++|+|||.+.+..+|+.+++++.+.+.+|++++|++++++++++|||||++|||+++...++|||++
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 HHHHHHHHHHHHHHhccccHHHHHHhHHHHHHHHHHHHhCcEEeecCHHHHHHHHHhhhh
Q 032349 81 LECIHLFVEILDHFFSNVCELDLVFNFHKVYLILDEFILAGELQETSKRAIIERMGELEK 140 (142)
Q Consensus 81 le~l~~~v~~l~~~f~~v~e~~i~~nf~~v~~lLDE~id~G~~~etd~~~i~~~i~~~~~ 140 (142)
+|++|+++++|+.|||+|||.|+++||.++|.+|||++-+|-++||+.+...+-++.+|-
T Consensus 81 LE~IH~~vE~lDkYFg~VCELDiiFNfekay~ILde~~~~g~~~e~~k~~~~~~i~~ad~ 140 (145)
T KOG0934|consen 81 LEFIHNYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEIQETSKNDVLKAIAQADL 140 (145)
T ss_pred HHHHHHHHHHHHHHhccceeeEEEEehHhHHHHHHHHhcCcchHhhhcccHHHHHHHhhh
Confidence 999999999999999999999999999999999999999999999999998888877664
No 5
>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.9e-37 Score=212.37 Aligned_cols=142 Identities=70% Similarity=1.122 Sum_probs=133.6
Q ss_pred CeEEEEeecCCCCeeEEecCCCCChhhHHHHHHHHHHHHhcCCCCCCceEEeCCeEEEEE-EeCCEEEEEEecCCcCHHH
Q 032349 1 MIRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRLVVNRDPKFTNFVEFRTHKVIYR-RYAGLFFSLCVDITDNELA 79 (142)
Q Consensus 1 MI~~i~iln~~G~~~l~k~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~-~~~~l~~~~~~~~~~Nel~ 79 (142)
||+++++.|++|+++++|||-+.+.+++++++.++++.+..|+.+..++++..+.+.+|+ +|++|||+.+++.-+||++
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 899999999999999999999888888899999999999999988877777776666655 9999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhccccHHHHHHhHHHHHHHHHHHHhCcEEeecCHHHHHHHHHhhhhcC
Q 032349 80 YLECIHLFVEILDHFFSNVCELDLVFNFHKVYLILDEFILAGELQETSKRAIIERMGELEKLE 142 (142)
Q Consensus 80 ~le~l~~~v~~l~~~f~~v~e~~i~~nf~~v~~lLDE~id~G~~~etd~~~i~~~i~~~~~~~ 142 (142)
.++-+|.|+++|++||+++||.++.+||.+||.++|||+-+|.++||+...+++|+.+.++++
T Consensus 81 yLe~IHlFVEvLd~fF~NVCELDlvFNFyKVy~i~DEm~l~GEi~Etsk~~vlerl~~L~~Le 143 (143)
T KOG0935|consen 81 YLEHIHLFVEVLDEFFHNVCELDLVFNFYKVYTIVDEMFLAGEIRETSKTKVLERLLMLQSLE 143 (143)
T ss_pred HHHHHHHHHHHHHHHhccccceeeeeeeeeHHHHHHHHHHhhhhhhhhHHHHHHHHHHHhccC
Confidence 999999999999999999999999999999999999999999999999999999999998864
No 6
>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.97 E-value=2.1e-31 Score=190.47 Aligned_cols=134 Identities=24% Similarity=0.369 Sum_probs=124.2
Q ss_pred eEEEEeecCCCCeeEEecCCCC--C-hhhHHHHHHHHHHHHhcCCCCCCceEEeCCeEEEEEEeCCEEEEEEecCCcCHH
Q 032349 2 IRFILLQNRQGKTRLAKYYVPL--E-DSEKHKVEYEVHRLVVNRDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNEL 78 (142)
Q Consensus 2 I~~i~iln~~G~~~l~k~Y~~~--~-~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~~~~~~~~~~Nel 78 (142)
+++++|+|++|+|+++|||.+. + -++|+++|+.+|++++. +.+.|..++|..+||+..-||+|+++++.+|||+
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 6899999999999999999864 3 56789999999988754 2368999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhcc-ccHHHHHHhHHHHHHHHHHHHhCcEEeecCHHHHHHHHHhh
Q 032349 79 AYLECIHLFVEILDHFFSN-VCELDLVFNFHKVYLILDEFILAGELQETSKRAIIERMGEL 138 (142)
Q Consensus 79 ~~le~l~~~v~~l~~~f~~-v~e~~i~~nf~~v~~lLDE~id~G~~~etd~~~i~~~i~~~ 138 (142)
++.+.|+++.++++..+++ +.+..+++|++.+++++||++|+|.++||||+.|+.|++..
T Consensus 86 ~L~svL~~l~dal~llLr~nveKr~llEN~D~i~L~~DEiiD~GvILEtdp~~ia~rv~~~ 146 (175)
T KOG3343|consen 86 MLMSVLTCLFDALSLLLRKNVEKRELLENLDLIFLALDEIIDGGVILETDPNQIAQRVALR 146 (175)
T ss_pred HHHHHHHHHHHHHHHHHHhChhHHHHHhhhccceeehhhhccCceEEecCHHHHHHHhccC
Confidence 9999999999999999976 89999999999999999999999999999999999999864
No 7
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.96 E-value=9.6e-30 Score=201.12 Aligned_cols=134 Identities=19% Similarity=0.241 Sum_probs=122.0
Q ss_pred CeEEEEeecCCCCeeEEecCCCCChhhHHHHHHHHHHH-HhcCCCCCCceEEeCCeEEEEEEeCCEEEEEEecCCcCHHH
Q 032349 1 MIRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRL-VVNRDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNELA 79 (142)
Q Consensus 1 MI~~i~iln~~G~~~l~k~Y~~~~~~~~~~~~~~~~~~-~~~~~~~~~~i~~~~~~~~vy~~~~~l~~~~~~~~~~Nel~ 79 (142)
||+++|++|.+|++++.|.|++.. ++-..++|+. ++.+....||+..+|+++++|.+..+||+++++++|.|..+
T Consensus 1 misglfi~n~rGevlink~fr~dl----krs~~diFRv~vi~n~d~r~PV~~igsttf~~~r~~nl~lvaitksN~Nva~ 76 (446)
T KOG0938|consen 1 MISGLFIYNLRGEVLINKTFRDDL----KRSIVDIFRVQVINNLDVRSPVLTIGSTTFHHIRSSNLWLVAITKSNANVAA 76 (446)
T ss_pred CcceEEEEeccCcEEEehhhhhhh----hhhHHHHHHHhhhhccccCCCeeEecceeEEEEeeccEEEEEEecCCCchhh
Confidence 999999999999999999999765 3344455554 66665567999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhccccHHHHHHhHHHHHHHHHHHHhCcEEeecCHHHHHHHHHhh
Q 032349 80 YLECIHLFVEILDHFFSNVCELDLVFNFHKVYLILDEFILAGELQETSKRAIIERMGEL 138 (142)
Q Consensus 80 ~le~l~~~v~~l~~~f~~v~e~~i~~nf~~v~~lLDE~id~G~~~etd~~~i~~~i~~~ 138 (142)
++|||..+.+++.+|||..+|+.|++||..+|++||||+|+|+||+|+|++++..++.+
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 99999999999999999999999999999999999999999999999999999988753
No 8
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.89 E-value=4e-23 Score=164.54 Aligned_cols=134 Identities=20% Similarity=0.181 Sum_probs=115.1
Q ss_pred CeEEEEeecCCCCeeEEecCCCCChhhHHHHHHHHHHHHhc--CCCCCCceEEeCCeEEEEEEeCCEEEEEEecCCcCHH
Q 032349 1 MIRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRLVVN--RDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNEL 78 (142)
Q Consensus 1 MI~~i~iln~~G~~~l~k~Y~~~~~~~~~~~~~~~~~~~~~--~~~~~~~i~~~~~~~~vy~~~~~l~~~~~~~~~~Nel 78 (142)
||+++|+.|.+|+.+++|.|+.... .+.++..++..-.+ +.++..|++..+.+.+.-.-..+++|++++..+..||
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 MILSIFLIDTSGDLLLEKHLKGSTV--VRSICDYFFEDQSSDDDLEHVPPVISTPHHYLFSVYRDLIFFCAVSTVETPPL 78 (418)
T ss_pred CeeEEEEEcCCchhhhhHhhCCcee--eeehHHHHHHhhhhccccccCCceecCCceeeeeeeccCcEEEEEEeccCCCh
Confidence 9999999999999999999994221 15677777766433 3344567777777777766667899999999999999
Q ss_pred HHHHHHHHHHHHHHHHhccccHHHHHHhHHHHHHHHHHHHhCcEEeecCHHHHHHHHH
Q 032349 79 AYLECIHLFVEILDHFFSNVCELDLVFNFHKVYLILDEFILAGELQETSKRAIIERMG 136 (142)
Q Consensus 79 ~~le~l~~~v~~l~~~f~~v~e~~i~~nf~~v~~lLDE~id~G~~~etd~~~i~~~i~ 136 (142)
++.|||+++++++..|||.++|..|++|++.||++||||+|+|+|..||++.+.+-|+
T Consensus 79 ~~iefL~rv~dv~~eyFg~~s~~~Ik~N~~vv~ell~emiDnGfpl~tE~NiLke~i~ 136 (418)
T KOG2740|consen 79 MVIEFLHRVVDVLLEYFGGLSESKIKDNVVVVYELLDEMIDNGFPLVTEPNILKELIP 136 (418)
T ss_pred hHHHHHHHHHHHHHHHhcccCHhHhhcceeeHHHHHHHHHHcCCCcccChhHHHhhcC
Confidence 9999999999999999999999999999999999999999999999999999888765
No 9
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.88 E-value=1.2e-21 Score=159.65 Aligned_cols=134 Identities=14% Similarity=0.191 Sum_probs=118.9
Q ss_pred eEEEEeecCCCCeeEEecCCCCChhhHHHHHHHHHHHHhcC--CCCCCceEEeCCeEEEEEEeCCEEEEEEecCCcCHHH
Q 032349 2 IRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRLVVNR--DPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNELA 79 (142)
Q Consensus 2 I~~i~iln~~G~~~l~k~Y~~~~~~~~~~~~~~~~~~~~~~--~~~~~~i~~~~~~~~vy~~~~~l~~~~~~~~~~Nel~ 79 (142)
+++++++|.+|+++++|.|+.... ......|+.++... .....|++.++|..++|.+++++|++++++.+.|+..
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 ASAVFILDHKGEVLISRDYRGDVP---MSSTEKFFRKLFEKEEGDESPPFLVHDGSRFIHIKHSNLYLVAGTRPNVSAAL 77 (424)
T ss_pred CceEEEEcCCCcEeEeecccccCC---hhhhhhHHHHHhhhcccCCCCCeEEeCCceEEEEeecceEEEEEeccCCCHHH
Confidence 579999999999999999996531 34455666554432 2334799999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhccccHHHHHHhHHHHHHHHHHHHhCcEEeecCHHHHHHHHHhh
Q 032349 80 YLECIHLFVEILDHFFSNVCELDLVFNFHKVYLILDEFILAGELQETSKRAIIERMGEL 138 (142)
Q Consensus 80 ~le~l~~~v~~l~~~f~~v~e~~i~~nf~~v~~lLDE~id~G~~~etd~~~i~~~i~~~ 138 (142)
+++||+++++++.+||+.+.|..+.+||+.+|++|||++|.|+||.|+++.+.+.+++.
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 99999999999999999999999999999999999999999999999999999998865
No 10
>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=99.86 E-value=2.7e-21 Score=138.33 Aligned_cols=133 Identities=18% Similarity=0.277 Sum_probs=119.8
Q ss_pred eEEEEeecCCCCeeEEecCCCCC-----------hhhHHHHHHHHHHHHhcCCCCCCceEEeCCeEEEEEEeCCEEEEEE
Q 032349 2 IRFILLQNRQGKTRLAKYYVPLE-----------DSEKHKVEYEVHRLVVNRDPKFTNFVEFRTHKVIYRRYAGLFFSLC 70 (142)
Q Consensus 2 I~~i~iln~~G~~~l~k~Y~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~~~~~ 70 (142)
+.|++|+|++|++++.|||.|+. -++++.+++.++++.... +..|..+.+..++|+++-|+.++.+
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 68999999999999999998753 235677888888876532 3588999999999999999999999
Q ss_pred ecCCcCHHHHHHHHHHHHHHHHHHhccc-cHHHHHHhHHHHHHHHHHHHhCcEEeecCHHHHHHHHHh
Q 032349 71 VDITDNELAYLECIHLFVEILDHFFSNV-CELDLVFNFHKVYLILDEFILAGELQETSKRAIIERMGE 137 (142)
Q Consensus 71 ~~~~~Nel~~le~l~~~v~~l~~~f~~v-~e~~i~~nf~~v~~lLDE~id~G~~~etd~~~i~~~i~~ 137 (142)
++-++||.++-+.+..+-.+|.-.++.. .++.+.+|++.+..+.||.+|+|.+++|+++.|+.|++.
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 9999999999999999999999999985 677799999999999999999999999999999999875
No 11
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.24 E-value=1.4e-10 Score=95.23 Aligned_cols=134 Identities=19% Similarity=0.292 Sum_probs=117.2
Q ss_pred eEEEEeecCCCCeeEEecCCCCChhhHHHHHHHHHHHHhcCCCCCCceEEeCCeEEEEEEeCCEEEEEEecCCcCHHHHH
Q 032349 2 IRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRLVVNRDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNELAYL 81 (142)
Q Consensus 2 I~~i~iln~~G~~~l~k~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~~~~~~~~~~Nel~~l 81 (142)
+-+.-+.+++|+.+++|.|+.++..+-..+..+|.+.+.. .++..+++-+++++||+...++|++.+|..+.|-|--+
T Consensus 3 vlaa~i~t~~Gk~ivsRqf~~Msr~RIEgLl~aFpkLv~~--~~qhT~vEt~~VRYVYqP~d~lY~vLITtk~SNIleDl 80 (512)
T KOG2635|consen 3 VLAASINTKTGKAIVSRQFREMSRSRIEGLLAAFPKLVSA--GKQHTFVETDSVRYVYQPLDNLYIVLITTKQSNILEDL 80 (512)
T ss_pred EEEEEEeecCCceeeehHhHhhhHHHHHHHHHHhHHhhcc--CCCccEEecccEEEEEEecccEEEEEEeccccchhhHH
Confidence 4466778899999999999988755545566777755542 23468999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhccccHHHHHHhHHHHHHHHHHHHhCcEEeecCHHHHHHHHHh
Q 032349 82 ECIHLFVEILDHFFSNVCELDLVFNFHKVYLILDEFILAGELQETSKRAIIERMGE 137 (142)
Q Consensus 82 e~l~~~v~~l~~~f~~v~e~~i~~nf~~v~~lLDE~id~G~~~etd~~~i~~~i~~ 137 (142)
+.|+.|..+...|+..+.|+.|.+|--.....+||++--||-...+...|+.++.|
T Consensus 81 ~TL~Lfskvipey~~slde~eI~~~~FelifAFDEivsLGyre~v~laQikty~eM 136 (512)
T KOG2635|consen 81 ETLRLFSKVIPEYCSSLDEKEILENAFELIFAFDEIVSLGYRENVNLAQIKTYLEM 136 (512)
T ss_pred HHHHHHHHhchhhhhhhhHHHHHHhhhhhhhccchhhhhcccccccHHHhhhhhcc
Confidence 99999999999999999999999999999999999999999999998888877654
No 12
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=97.49 E-value=0.013 Score=43.98 Aligned_cols=79 Identities=19% Similarity=0.331 Sum_probs=70.4
Q ss_pred CeEEEEEEeCCEEEEEEecCCcCHHHHHHHHHHHHHHHHHHhcccc-HHHHHHhHHHHHHHHHHHHhCcEEeecCHHHHH
Q 032349 54 THKVIYRRYAGLFFSLCVDITDNELAYLECIHLFVEILDHFFSNVC-ELDLVFNFHKVYLILDEFILAGELQETSKRAII 132 (142)
Q Consensus 54 ~~~~vy~~~~~l~~~~~~~~~~Nel~~le~l~~~v~~l~~~f~~v~-e~~i~~nf~~v~~lLDE~id~G~~~etd~~~i~ 132 (142)
...++|....++.|..+.+..||-++.-.+|+.++..+..+++.++ -..+...-+.+..+|+..+=.|-.+--+.+.+.
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 4577899999999999999999999999999999999999997754 477888999999999999999988888877744
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=96.54 E-value=0.068 Score=44.69 Aligned_cols=86 Identities=7% Similarity=0.173 Sum_probs=57.3
Q ss_pred EEEEeecCCCCeeEEecCCCCChhhHHHHHHHHHHHHh---cCCCCCCceEEeCCeEEEEEEeCCEEEEEEecCCcCHHH
Q 032349 3 RFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRLVV---NRDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNELA 79 (142)
Q Consensus 3 ~~i~iln~~G~~~l~k~Y~~~~~~~~~~~~~~~~~~~~---~~~~~~~~i~~~~~~~~vy~~~~~l~~~~~~~~~~Nel~ 79 (142)
+-+||++..||+++++| .++++-..+..-+...++ ..+ ..-.-+..|++++|+...+-|+++++++.+|++-.
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---GDEDKLSSLMGVIQAIISFFQSNG-DELRSIRAGDHRIVFLNRGPLILVAVSKTGESESQ 87 (415)
T ss_pred CeEEEECCCCceeEEec---CChHHHHHHHHHHHHHHHHHHhCC-CcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCHHH
Confidence 45899999999999999 222222233333333322 222 21234567899999999999999999999999877
Q ss_pred HHHHHHHHHHHHH
Q 032349 80 YLECIHLFVEILD 92 (142)
Q Consensus 80 ~le~l~~~v~~l~ 92 (142)
+..-|+.+...+-
T Consensus 88 l~~qL~~ly~qil 100 (415)
T PF03164_consen 88 LRKQLDYLYSQIL 100 (415)
T ss_pred HHHHHHHHHHHHH
Confidence 7655554444333
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=95.04 E-value=0.75 Score=32.00 Aligned_cols=92 Identities=10% Similarity=0.084 Sum_probs=60.6
Q ss_pred eEEEEeecCCCCeeEEecCCCCCh-hhHHHHHHHHHHHH---hc--CCCCCCceEEeCCeEEEEEEeCCEEEEEEecCCc
Q 032349 2 IRFILLQNRQGKTRLAKYYVPLED-SEKHKVEYEVHRLV---VN--RDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITD 75 (142)
Q Consensus 2 I~~i~iln~~G~~~l~k~Y~~~~~-~~~~~~~~~~~~~~---~~--~~~~~~~i~~~~~~~~vy~~~~~l~~~~~~~~~~ 75 (142)
+.++++-|++|=+++.=...+... .-+..+...+-... .+ -.....-+..++++.+++.....+++.++++++.
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 679999999998887644443322 11233333322111 11 1112245667899999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHHHH
Q 032349 76 NELAYLECIHLFVEILDH 93 (142)
Q Consensus 76 Nel~~le~l~~~v~~l~~ 93 (142)
|--+++.+-+.+...++.
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 999999988887777764
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=94.10 E-value=1.3 Score=31.56 Aligned_cols=93 Identities=19% Similarity=0.207 Sum_probs=53.6
Q ss_pred eEEEEeecCCCCeeEEecCCCC--------ChhhHHHHHHHHHH------HHhcCCC-----CCCce--EEeCCeEEE-E
Q 032349 2 IRFILLQNRQGKTRLAKYYVPL--------EDSEKHKVEYEVHR------LVVNRDP-----KFTNF--VEFRTHKVI-Y 59 (142)
Q Consensus 2 I~~i~iln~~G~~~l~k~Y~~~--------~~~~~~~~~~~~~~------~~~~~~~-----~~~~i--~~~~~~~~v-y 59 (142)
|.+++|+|+.|..++.|-|... ...+++.+-.-++. ++...+. ..+.+ +..+.+++- |
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 6899999999999999988742 22334444444433 2222111 11223 345677666 4
Q ss_pred EEeCCEEEEEEecCCcCHHHHHHHHHHHHHHHHHHh
Q 032349 60 RRYAGLFFSLCVDITDNELAYLECIHLFVEILDHFF 95 (142)
Q Consensus 60 ~~~~~l~~~~~~~~~~Nel~~le~l~~~v~~l~~~f 95 (142)
..--++-|++++|.+... ..-++++.+.+...+|-
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 445689999999998854 34556677778777763
No 16
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.93 E-value=3.3 Score=31.73 Aligned_cols=71 Identities=8% Similarity=0.128 Sum_probs=58.2
Q ss_pred hhHHHHHHHHHHHHhcCCCCCCceEEeCCeEEEEEEeCCEEEEEEecCCcCHHHHHHHHHHHHHHHHHHhcc
Q 032349 26 SEKHKVEYEVHRLVVNRDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNELAYLECIHLFVEILDHFFSN 97 (142)
Q Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~~~~~~~~~~Nel~~le~l~~~v~~l~~~f~~ 97 (142)
.+.++-.+.+++++...++..|. ++-|.+.+-|...+++..++.++.+.+--+.+.+|..+.+-+.+-+++
T Consensus 31 ~e~r~q~K~L~kkLs~~s~~r~S-ietg~f~fHfli~~~Vcylvicd~~yP~kLAF~YLedL~~EF~~~~~~ 101 (216)
T KOG0862|consen 31 LEYRQQAKSLFKKLSQQSPTRCS-IETGPFVFHFLIESGVCYLVICDKSYPRKLAFSYLEDLAQEFDKSYGK 101 (216)
T ss_pred HHHHHHHHHHHHhccCCCCcccc-cccCCeEEEEEecCCEEEEEEecCCCcHHHHHHHHHHHHHHHHHhccc
Confidence 45566677777777554344454 566778999999999999999999999999999999999999988875
No 17
>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=92.22 E-value=1.7 Score=27.61 Aligned_cols=49 Identities=8% Similarity=-0.023 Sum_probs=42.8
Q ss_pred ceEEeCCeEEEEEEeCCEEEEEEecCCcCHHHHHHHHHHHHHHHHHHhc
Q 032349 48 NFVEFRTHKVIYRRYAGLFFSLCVDITDNELAYLECIHLFVEILDHFFS 96 (142)
Q Consensus 48 ~i~~~~~~~~vy~~~~~l~~~~~~~~~~Nel~~le~l~~~v~~l~~~f~ 96 (142)
-.+..+++.+-|...+++.++++++.+.+.-..+.||..+.+-+..-++
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 3566888988888899999999999999999999999999888888776
No 18
>KOG0997 consensus Uncharacterized conserved protein Sand [Function unknown]
Probab=88.05 E-value=7 Score=33.56 Aligned_cols=80 Identities=10% Similarity=0.071 Sum_probs=50.5
Q ss_pred EEEeecCCCCeeEEecCCCCChhhHHHHHHHHHHHHhcCCCCCCceEEeCCeEEEEEEeCCEEEEEEecCCcCHHHHHHH
Q 032349 4 FILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRLVVNRDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNELAYLEC 83 (142)
Q Consensus 4 ~i~iln~~G~~~l~k~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~~~~~~~~~~Nel~~le~ 83 (142)
-+||+...|+++++++=.............++..-+...... --.+..+|+++++-+.+-++++++...+...--++.-
T Consensus 119 hifilseaGKPiyS~~gs~e~l~stmGv~~alISf~q~~~~~-i~si~a~g~k~vfl~kspl~LvA~s~t~~Sa~qL~~q 197 (523)
T KOG0997|consen 119 HIFILSEAGKPIYSRHGSDEALSSTMGVMQALISFFQVSGLA-ITSIHAFGNKLVFLQKSPLLLVAVSRTSQSAAQLLQQ 197 (523)
T ss_pred eEEEEecCCCceeeecCcHHHHHHHHHHHHHHHHHHhhCCce-EEEEEecCceEEEEecCcEEEEEEcccccCHHHHHHH
Confidence 489999999999999865422211122233332222112222 1234568899999999999999999988766555443
Q ss_pred H
Q 032349 84 I 84 (142)
Q Consensus 84 l 84 (142)
|
T Consensus 198 L 198 (523)
T KOG0997|consen 198 L 198 (523)
T ss_pred H
Confidence 3
No 19
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=87.77 E-value=10 Score=28.84 Aligned_cols=87 Identities=9% Similarity=-0.003 Sum_probs=59.3
Q ss_pred eecCCCCeeEEecCCC-CChhhHHHHHHHHHHHHhcCCCCCCceEEeCCeEEEEEEeCCEEEEEEecCCcCHHHHHHHHH
Q 032349 7 LQNRQGKTRLAKYYVP-LEDSEKHKVEYEVHRLVVNRDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNELAYLECIH 85 (142)
Q Consensus 7 iln~~G~~~l~k~Y~~-~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~~~~~~~~~~Nel~~le~l~ 85 (142)
-+=.+|-++|++|=.- ... ..+.+++-+++.+.++ .---..+|+|.+-|.+-+++.++++++.+.---.-+.||.
T Consensus 6 s~VARGTvvLaeft~~~gNf---~sva~qiL~klp~~~n-~k~tYs~d~y~Fh~l~~dg~tylcvadds~gR~ipfaFLe 81 (217)
T KOG0859|consen 6 SFVARGTVILAEFTEFSGNF---SSIAAQILQKLPSSSN-SKFTYSCDGYTFHYLVEDGLTYLCVADDSAGRQIPFAFLE 81 (217)
T ss_pred EEEecceEEEEeeeeccCCH---HHHHHHHHHhCCCCCC-CceEEecCCeEEEEEEeCCeEEEEEEeccccccccHHHHH
Confidence 3447899999997542 111 2333344444432221 1123467999999999999999999998888888888998
Q ss_pred HHHHHHHHHhcc
Q 032349 86 LFVEILDHFFSN 97 (142)
Q Consensus 86 ~~v~~l~~~f~~ 97 (142)
.+.+-+..-+|.
T Consensus 82 ~Ik~~F~k~YG~ 93 (217)
T KOG0859|consen 82 RIKEDFKKRYGG 93 (217)
T ss_pred HHHHHHHHHhcc
Confidence 887776665553
No 20
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=85.78 E-value=23 Score=30.79 Aligned_cols=112 Identities=12% Similarity=0.064 Sum_probs=65.5
Q ss_pred CeEEEEeecCCCCeeEEecCCCCChhhHHHHHHHHHHH-HhcCCCCCCceEEeCCeEEEEEEeCC--EEEEEEecCCcCH
Q 032349 1 MIRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRL-VVNRDPKFTNFVEFRTHKVIYRRYAG--LFFSLCVDITDNE 77 (142)
Q Consensus 1 MI~~i~iln~~G~~~l~k~Y~~~~~~~~~~~~~~~~~~-~~~~~~~~~~i~~~~~~~~vy~~~~~--l~~~~~~~~~~Ne 77 (142)
|+-.+.|+++.|-++....=-..... .....+.+. +.++.+...+ +.++.+++-|...++ +.|+++-..--+=
T Consensus 1 Mld~faIFtkgG~vLw~~~~~~~~~~---~~in~lI~~~ll~er~~~~~-~~~~~yTlk~q~~N~~~lvfvvvfqki~~L 76 (587)
T KOG0781|consen 1 MLDQFAIFTKGGLVLWCYQEVGDNLK---GPINALIRSVLLSERGGVNS-FTFEAYTLKYQLDNQYSLVFVVVFQKILTL 76 (587)
T ss_pred CcceeeeecCCcEEEEEecccchhcc---chHHHHHHHHHHHhhcCccc-CchhheeEeeeecCCccEEEEEEEeccchh
Confidence 88999999999977643221111111 123344443 3332222223 778888888888775 4456665544454
Q ss_pred HHHHHHHHHHHHHHHHHhccccHHHHHHh-HHHHHHHHHH
Q 032349 78 LAYLECIHLFVEILDHFFSNVCELDLVFN-FHKVYLILDE 116 (142)
Q Consensus 78 l~~le~l~~~v~~l~~~f~~v~e~~i~~n-f~~v~~lLDE 116 (142)
..+-.+|....+.+..-|+..+-..++-| ++...++|++
T Consensus 77 ~yv~~ll~~v~~~f~e~~~~~~~~~l~~n~~~~~~e~lk~ 116 (587)
T KOG0781|consen 77 TYVDKLLNDVLNLFREKYDTQSALSLLNNTFDFQEELLKL 116 (587)
T ss_pred hhHHHHHHHHHHHHHHHhccchHHHhhhhhHHHHHHHHHH
Confidence 55566677777777776766555666666 4455666654
No 21
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=82.49 E-value=14 Score=25.71 Aligned_cols=91 Identities=15% Similarity=0.203 Sum_probs=53.2
Q ss_pred eEEEEeecCCCCeeEEecCCCCChh----hHHHH---HHHHHHHHhcCCC--CCC--ceEEeCC-eEEEEEEeCCEEEEE
Q 032349 2 IRFILLQNRQGKTRLAKYYVPLEDS----EKHKV---EYEVHRLVVNRDP--KFT--NFVEFRT-HKVIYRRYAGLFFSL 69 (142)
Q Consensus 2 I~~i~iln~~G~~~l~k~Y~~~~~~----~~~~~---~~~~~~~~~~~~~--~~~--~i~~~~~-~~~vy~~~~~l~~~~ 69 (142)
+.+++|.|++|..++.|-|.+...+ +---+ ...++....+..+ ..+ ..+..++ ...+|+..-++-|++
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 7899999999999999999532110 00000 1111111111111 112 2444555 356799999999999
Q ss_pred Ee-cCCcCHHHHHHHHHHHHHHHHHHh
Q 032349 70 CV-DITDNELAYLECIHLFVEILDHFF 95 (142)
Q Consensus 70 ~~-~~~~Nel~~le~l~~~v~~l~~~f 95 (142)
++ +.-.|.++- ++.+++...+|-
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 455555443 667777777764
No 22
>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=65.41 E-value=63 Score=25.16 Aligned_cols=50 Identities=8% Similarity=0.049 Sum_probs=32.6
Q ss_pred ceEEeCCeEEEEEEeC--CEEEEEEecCCcCHHHHHHHHHHHHHHHHHHhcc
Q 032349 48 NFVEFRTHKVIYRRYA--GLFFSLCVDITDNELAYLECIHLFVEILDHFFSN 97 (142)
Q Consensus 48 ~i~~~~~~~~vy~~~~--~l~~~~~~~~~~Nel~~le~l~~~v~~l~~~f~~ 97 (142)
+-+.+++|.+=|+-.+ +|.|+|+-..=-.-..+-+||..+...|...|+.
T Consensus 20 ~~~~~d~y~lkw~~~Ne~~LvfVvvYq~il~l~yvd~LL~~v~~~F~~~y~~ 71 (279)
T PF04086_consen 20 SSFTYDNYTLKWTLDNELGLVFVVVYQKILQLTYVDKLLDDVKKEFVKLYKN 71 (279)
T ss_dssp --------EEEEEEETTTTEEEEEEES-GGGHHHHHHHHHHHHHHHHHHTHH
T ss_pred CceeEcCEEEEEEEeccCCEEEeeeecccccchHHHHHHHHHHHHHHHHHhH
Confidence 3478899999999988 6788888887777777777887777777776665
No 23
>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=65.28 E-value=20 Score=26.23 Aligned_cols=50 Identities=16% Similarity=0.161 Sum_probs=37.4
Q ss_pred HHHHHHHHhccccHHHHHHhHHHHHHHHHHHHhCcEEeec------CHHHHHHHHH
Q 032349 87 FVEILDHFFSNVCELDLVFNFHKVYLILDEFILAGELQET------SKRAIIERMG 136 (142)
Q Consensus 87 ~v~~l~~~f~~v~e~~i~~nf~~v~~lLDE~id~G~~~et------d~~~i~~~i~ 136 (142)
+-+.|+.+++.+.+.+..+...-.-+.+||-..+|.-.+- ||+.+++.+.
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 FLNELEKYLKKLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIAREIL 61 (181)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHHHH
Confidence 3345777888889999988888888888888887764443 6777766655
No 24
>COG3322 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]
Probab=59.54 E-value=8.7 Score=30.91 Aligned_cols=23 Identities=13% Similarity=0.117 Sum_probs=19.8
Q ss_pred eEEEEeecCCCCeeEEecCCCCC
Q 032349 2 IRFILLQNRQGKTRLAKYYVPLE 24 (142)
Q Consensus 2 I~~i~iln~~G~~~l~k~Y~~~~ 24 (142)
+.++|++|++|+++++|.+++.+
T Consensus 104 ~d~vf~vd~~G~~vy~~~~d~~t 126 (295)
T COG3322 104 LDGVFVVDPSGKLVYSKLVDQET 126 (295)
T ss_pred ccEEEEECCCCCEEEEeeecccc
Confidence 35899999999999999998643
No 25
>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=58.97 E-value=65 Score=23.18 Aligned_cols=71 Identities=10% Similarity=0.167 Sum_probs=32.1
Q ss_pred CeEEEEeecCCCCeeEEecCCCCChhhHHHHHHHHHHHHhcC----CCC--CCceEEeC-------CeEEEEEE--eCCE
Q 032349 1 MIRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRLVVNR----DPK--FTNFVEFR-------THKVIYRR--YAGL 65 (142)
Q Consensus 1 MI~~i~iln~~G~~~l~k~Y~~~~~~~~~~~~~~~~~~~~~~----~~~--~~~i~~~~-------~~~~vy~~--~~~l 65 (142)
|+-.+-|+.++|++++. |.....+-......+|...+++. .+. ...+..+. +++..|+- .+.|
T Consensus 1 MfdQlaIFTpqGqvLyq--yN~~gKKFsE~QiN~FIs~lItsP~~~~e~~~~~k~~~i~s~~~~~~~f~~mfh~sKQPeL 78 (148)
T PF09201_consen 1 MFDQLAIFTPQGQVLYQ--YNCLGKKFSETQINAFISHLITSPVTKKEDSSKSKFLTISSEKKNSRSFSAMFHISKQPEL 78 (148)
T ss_dssp ---EEEEE-TT-BEEEE--EETTS----HHHHHHHHHHHHHS---GGGTT--EEEEE-----------EEEEEEETTTTE
T ss_pred CcceeEEeccCceEEEE--ecccchHHHHHHHHHHHHHHhcCCCcccCCCcceeeEEecccccCCCChheeeeecCCCcE
Confidence 88999999999999864 33322111112223333333221 111 13344433 66666554 5799
Q ss_pred EEEEEecC
Q 032349 66 FFSLCVDI 73 (142)
Q Consensus 66 ~~~~~~~~ 73 (142)
|++++-.+
T Consensus 79 y~VvTyae 86 (148)
T PF09201_consen 79 YYVVTYAE 86 (148)
T ss_dssp EEEEEESS
T ss_pred EEEEEecc
Confidence 99998875
No 26
>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=52.00 E-value=55 Score=22.68 Aligned_cols=21 Identities=19% Similarity=0.357 Sum_probs=17.3
Q ss_pred eEEEEeecCCCCeeE--EecCCC
Q 032349 2 IRFILLQNRQGKTRL--AKYYVP 22 (142)
Q Consensus 2 I~~i~iln~~G~~~l--~k~Y~~ 22 (142)
+.+++++|.+|++++ ++.+..
T Consensus 50 ~d~~~~~d~~g~~~~~~~~~~~~ 72 (161)
T PF05228_consen 50 LDLIFILDPDGRVLYSSSKGYDF 72 (161)
T ss_pred ccEEEEEcCCCCEEEEeccCccc
Confidence 468999999999998 666654
No 27
>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=51.98 E-value=27 Score=24.16 Aligned_cols=33 Identities=27% Similarity=0.317 Sum_probs=22.4
Q ss_pred HHHHHHHhccccHHHHHHhHHHHHHHHHHHHhCcEE
Q 032349 88 VEILDHFFSNVCELDLVFNFHKVYLILDEFILAGEL 123 (142)
Q Consensus 88 v~~l~~~f~~v~e~~i~~nf~~v~~lLDE~id~G~~ 123 (142)
.+.|.+=|+++. -.=|-..+|-.|+|++++|+.
T Consensus 38 Ld~lr~EFk~~G---y~P~hsEvYraLHeL~~dGil 70 (122)
T PF02334_consen 38 LDELRSEFKPLG---YRPNHSEVYRALHELVDDGIL 70 (122)
T ss_dssp HHHHHHHHTTTT-------HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHhhhcC---CCCCHHHHHHHHHHHHhhhHH
Confidence 344555566554 445778999999999999998
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=47.79 E-value=18 Score=17.47 Aligned_cols=18 Identities=22% Similarity=0.270 Sum_probs=14.5
Q ss_pred HhHHHHHHHHHHHHhCcE
Q 032349 105 FNFHKVYLILDEFILAGE 122 (142)
Q Consensus 105 ~nf~~v~~lLDE~id~G~ 122 (142)
.+++.+..+++||.+.|+
T Consensus 14 ~~~~~a~~~~~~M~~~g~ 31 (31)
T PF01535_consen 14 GQFEEALEVFDEMRERGI 31 (31)
T ss_pred chHHHHHHHHHHHhHCcC
Confidence 357788899999998874
No 29
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=45.07 E-value=1.1e+02 Score=21.79 Aligned_cols=85 Identities=15% Similarity=0.187 Sum_probs=49.3
Q ss_pred eEEEEeecCCCCeeEEecCCC-----CChhh-HHHHH------HHHHHHHhcCCCCCCceEE--eCCeEEEEEEe-CCEE
Q 032349 2 IRFILLQNRQGKTRLAKYYVP-----LEDSE-KHKVE------YEVHRLVVNRDPKFTNFVE--FRTHKVIYRRY-AGLF 66 (142)
Q Consensus 2 I~~i~iln~~G~~~l~k~Y~~-----~~~~~-~~~~~------~~~~~~~~~~~~~~~~i~~--~~~~~~vy~~~-~~l~ 66 (142)
|.++.|+|+.|..++.+-|.. ...++ -+-.- +.+-+++...+.+ -.|.. -+.++.-|-.. .+|.
T Consensus 3 iy~~yIFdR~g~Cl~y~EW~r~~~s~~~~eee~KL~yGmlFSlkS~v~Kls~~d~k-~~f~sy~Ts~YklhfyeTptglk 81 (140)
T KOG3368|consen 3 IYNFYIFDRNGVCLFYREWNRTKQSGIPNEEEAKLMYGMLFSLKSFVSKLSPGDVK-DGFLSYKTSKYKLHFYETPTGLK 81 (140)
T ss_pred EEEEEEEcCCccEEEehhcccccccCCchhHHHHHHHHHHhhHHHHHHhcCCCCcc-cCeeEEeeceeEEEEEEcCCCcE
Confidence 789999999999999876642 11111 11111 2222233222211 22333 34566655544 4899
Q ss_pred EEEEecCCcCHHHHHHHHHHHHH
Q 032349 67 FSLCVDITDNELAYLECIHLFVE 89 (142)
Q Consensus 67 ~~~~~~~~~Nel~~le~l~~~v~ 89 (142)
|+..++..... +-++||.+..
T Consensus 82 ~vl~Tdpk~~~--ir~vLq~IYs 102 (140)
T KOG3368|consen 82 FVLNTDPKAGS--IRDVLQYIYS 102 (140)
T ss_pred EEEecCCCccc--HHHHHHHHHH
Confidence 99999877654 4677777766
No 30
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=44.38 E-value=20 Score=17.76 Aligned_cols=17 Identities=18% Similarity=0.221 Sum_probs=14.2
Q ss_pred hHHHHHHHHHHHHhCcE
Q 032349 106 NFHKVYLILDEFILAGE 122 (142)
Q Consensus 106 nf~~v~~lLDE~id~G~ 122 (142)
+++.+..++++|...|+
T Consensus 16 ~~~~a~~~~~~M~~~gv 32 (34)
T PF13812_consen 16 DPDAALQLFDEMKEQGV 32 (34)
T ss_pred CHHHHHHHHHHHHHhCC
Confidence 46778999999999885
No 31
>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=44.25 E-value=24 Score=23.15 Aligned_cols=29 Identities=21% Similarity=0.116 Sum_probs=23.3
Q ss_pred ccHHHHHHh----HHHHHHHHHHHHhCcEEeec
Q 032349 98 VCELDLVFN----FHKVYLILDEFILAGELQET 126 (142)
Q Consensus 98 v~e~~i~~n----f~~v~~lLDE~id~G~~~et 126 (142)
+.-..|... -..|..++|++++.|++..|
T Consensus 66 v~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsT 98 (102)
T PF08784_consen 66 VHVDEIAQQLGMSENEVRKALDFLSNEGHIYST 98 (102)
T ss_dssp EEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEES
T ss_pred ccHHHHHHHhCcCHHHHHHHHHHHHhCCeEecc
Confidence 555555554 47899999999999999988
No 32
>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=41.81 E-value=32 Score=20.14 Aligned_cols=15 Identities=33% Similarity=0.503 Sum_probs=11.0
Q ss_pred HHHHHHHHHhCcEEe
Q 032349 110 VYLILDEFILAGELQ 124 (142)
Q Consensus 110 v~~lLDE~id~G~~~ 124 (142)
.-..|||++..|.+.
T Consensus 15 L~dtLDeli~~~~I~ 29 (49)
T PF02268_consen 15 LTDTLDELIQEGKIT 29 (49)
T ss_dssp HHHHHHHHHHTTSS-
T ss_pred HHHHHHHHHHcCCCC
Confidence 346789999888775
No 33
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=40.07 E-value=1.6e+02 Score=22.12 Aligned_cols=45 Identities=13% Similarity=0.189 Sum_probs=34.8
Q ss_pred eEEeCCe-EEEEEEeCCEEEEEEecCCcCHHHHHHHHHHHHHHHHHHh
Q 032349 49 FVEFRTH-KVIYRRYAGLFFSLCVDITDNELAYLECIHLFVEILDHFF 95 (142)
Q Consensus 49 i~~~~~~-~~vy~~~~~l~~~~~~~~~~Nel~~le~l~~~v~~l~~~f 95 (142)
+++.+.. .++|+..-++-|+++++... -.+-.+|..+++.-.+|-
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 4555654 56788899999999998776 456778899999888873
No 34
>PF14903 WG_beta_rep: WG containing repeat
Probab=39.12 E-value=32 Score=17.48 Aligned_cols=17 Identities=18% Similarity=0.364 Sum_probs=14.3
Q ss_pred eecCCCCeeEEecCCCC
Q 032349 7 LQNRQGKTRLAKYYVPL 23 (142)
Q Consensus 7 iln~~G~~~l~k~Y~~~ 23 (142)
++|.+|++++..-|+..
T Consensus 3 ~id~~G~~vi~~~yd~i 19 (35)
T PF14903_consen 3 YIDKNGKIVIPPKYDEI 19 (35)
T ss_pred EEeCCCCEEEEccccCc
Confidence 57999999999888764
No 35
>PF08217 DUF1712: Fungal domain of unknown function (DUF1712); InterPro: IPR013176 The function of this fungal family of proteins is unknown.
Probab=35.76 E-value=3.2e+02 Score=24.31 Aligned_cols=73 Identities=14% Similarity=0.257 Sum_probs=48.1
Q ss_pred CCCCceEEeCCeEEE-EEEeCCEEEEEEec-------CCcCHHHHHHHHHHHHHHHHHHhccccHHHHHHhHHHHHHHHH
Q 032349 44 PKFTNFVEFRTHKVI-YRRYAGLFFSLCVD-------ITDNELAYLECIHLFVEILDHFFSNVCELDLVFNFHKVYLILD 115 (142)
Q Consensus 44 ~~~~~i~~~~~~~~v-y~~~~~l~~~~~~~-------~~~Nel~~le~l~~~v~~l~~~f~~v~e~~i~~nf~~v~~lLD 115 (142)
+..|..++-..++++ +..-++.|++++.+ .+..+-.+...|....+.+.-++|.++.. .++.......|+
T Consensus 55 ~~~~~~I~T~K~r~v~~e~Ep~~Wi~l~I~~~~~~~~~~~~~~~L~~~L~~~Y~~F~L~hGsfs~~--l~~r~~L~~~L~ 132 (604)
T PF08217_consen 55 DDPCDSIHTEKSRIVFYEPEPGFWIVLSINLPKEQSTKDGPEQYLLSVLKQAYSMFRLFHGSFSSL--LEGREKLKDRLE 132 (604)
T ss_pred CCcccceeecceEEEEEEecCCEEEEEEEecCcCCccccchHHHHHHHHHHHHHHHHHHcCCHHHh--cccHHHHHHHHH
Confidence 345777777776666 55568999988877 22344458899999999999998975432 114444444444
Q ss_pred HHH
Q 032349 116 EFI 118 (142)
Q Consensus 116 E~i 118 (142)
+-.
T Consensus 133 ~F~ 135 (604)
T PF08217_consen 133 DFF 135 (604)
T ss_pred HHH
Confidence 443
No 36
>COG1049 AcnB Aconitase B [Energy production and conversion]
Probab=34.86 E-value=66 Score=28.87 Aligned_cols=40 Identities=15% Similarity=0.228 Sum_probs=34.7
Q ss_pred ccHHHHHHhHHHHHHHHHHHHhCcEEeecCHHHHHHHHHhhhh
Q 032349 98 VCELDLVFNFHKVYLILDEFILAGELQETSKRAIIERMGELEK 140 (142)
Q Consensus 98 v~e~~i~~nf~~v~~lLDE~id~G~~~etd~~~i~~~i~~~~~ 140 (142)
++++.+++-...-..++..||+.||= |+.++..|+..+++
T Consensus 602 l~~e~iiEyL~sni~l~k~MIa~Gy~---d~rTL~rri~~me~ 641 (852)
T COG1049 602 LNKEPIIEYLKSNIVLLKWMIAEGYG---DARTLERRIDKMEA 641 (852)
T ss_pred cCchhHHHHHHHHHHHHHHHHHhccc---cHHHHHHHHHHHHH
Confidence 46788888888888899999999995 99999999987765
No 37
>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=34.56 E-value=1.2e+02 Score=22.35 Aligned_cols=19 Identities=32% Similarity=0.557 Sum_probs=16.6
Q ss_pred EEEEeecCCCCeeEEecCC
Q 032349 3 RFILLQNRQGKTRLAKYYV 21 (142)
Q Consensus 3 ~~i~iln~~G~~~l~k~Y~ 21 (142)
.+.|++|++|+++....|.
T Consensus 118 r~~fiID~~G~I~~~~~~~ 136 (203)
T cd03016 118 RAVFIIDPDKKIRLILYYP 136 (203)
T ss_pred eEEEEECCCCeEEEEEecC
Confidence 4689999999999888886
No 38
>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=34.34 E-value=37 Score=16.50 Aligned_cols=19 Identities=11% Similarity=0.179 Sum_probs=15.5
Q ss_pred hHHHHHHHHHHHHhCcEEe
Q 032349 106 NFHKVYLILDEFILAGELQ 124 (142)
Q Consensus 106 nf~~v~~lLDE~id~G~~~ 124 (142)
++..+..++++|...|...
T Consensus 15 ~~~~a~~~~~~M~~~g~~p 33 (35)
T TIGR00756 15 RVEEALELFKEMLERGIEP 33 (35)
T ss_pred CHHHHHHHHHHHHHcCCCC
Confidence 4678889999999988754
No 39
>PRK13190 putative peroxiredoxin; Provisional
Probab=33.67 E-value=1.1e+02 Score=22.65 Aligned_cols=21 Identities=19% Similarity=0.363 Sum_probs=17.8
Q ss_pred eEEEEeecCCCCeeEEecCCC
Q 032349 2 IRFILLQNRQGKTRLAKYYVP 22 (142)
Q Consensus 2 I~~i~iln~~G~~~l~k~Y~~ 22 (142)
+-+.|++|++|+++....|..
T Consensus 117 ~p~~fiId~~G~I~~~~~~~~ 137 (202)
T PRK13190 117 VRGVFIIDPNQIVRWMIYYPA 137 (202)
T ss_pred EeEEEEECCCCEEEEEEEeCC
Confidence 468899999999998887764
No 40
>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=30.40 E-value=46 Score=21.80 Aligned_cols=41 Identities=10% Similarity=0.104 Sum_probs=33.2
Q ss_pred HHHHHHhHHHHHHHHHHHHhCcEEeecCHHHHHHHHHhhhh
Q 032349 100 ELDLVFNFHKVYLILDEFILAGELQETSKRAIIERMGELEK 140 (142)
Q Consensus 100 e~~i~~nf~~v~~lLDE~id~G~~~etd~~~i~~~i~~~~~ 140 (142)
...++.+...|-=+||.+.++|++.+-+-++|.+.=+.+||
T Consensus 7 Re~LV~rI~~v~plLD~Ll~n~~it~E~y~~V~a~~T~qdk 47 (85)
T cd08324 7 RELLVTHIRNTQCLVDNLLKNDYFSTEDAEIVCACPTQPDK 47 (85)
T ss_pred HHHHHHHHHhhHHHHHHHhccCCccHHHHHHHHhCCCCHHH
Confidence 45677888888889999999999998888888776666655
No 41
>smart00571 DDT domain in different transcription and chromosome remodeling factors.
Probab=30.10 E-value=47 Score=20.08 Aligned_cols=16 Identities=25% Similarity=0.370 Sum_probs=14.4
Q ss_pred CHHHHHHHHHHHHHHH
Q 032349 76 NELAYLECIHLFVEIL 91 (142)
Q Consensus 76 Nel~~le~l~~~v~~l 91 (142)
+-++++|||+.+.++|
T Consensus 6 d~l~V~eFl~~F~~~L 21 (63)
T smart00571 6 DLLMVYEFLRSFGKVL 21 (63)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 5689999999999998
No 42
>PF13041 PPR_2: PPR repeat family
Probab=29.88 E-value=41 Score=18.68 Aligned_cols=22 Identities=14% Similarity=0.209 Sum_probs=18.3
Q ss_pred HhHHHHHHHHHHHHhCcEEeec
Q 032349 105 FNFHKVYLILDEFILAGELQET 126 (142)
Q Consensus 105 ~nf~~v~~lLDE~id~G~~~et 126 (142)
.+++.+..+++||...|+....
T Consensus 17 ~~~~~a~~l~~~M~~~g~~P~~ 38 (50)
T PF13041_consen 17 GKFEEALKLFKEMKKRGIKPDS 38 (50)
T ss_pred cCHHHHHHHHHHHHHcCCCCCH
Confidence 3678999999999999986644
No 43
>COG0450 AhpC Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=27.96 E-value=1.7e+02 Score=22.10 Aligned_cols=21 Identities=14% Similarity=0.072 Sum_probs=18.8
Q ss_pred eEEEEeecCCCCeeEEecCCC
Q 032349 2 IRFILLQNRQGKTRLAKYYVP 22 (142)
Q Consensus 2 I~~i~iln~~G~~~l~k~Y~~ 22 (142)
..++||+|++|.++..-+|..
T Consensus 124 ~R~~FIIDp~g~ir~~~v~~~ 144 (194)
T COG0450 124 LRGTFIIDPDGVIRHILVNPL 144 (194)
T ss_pred eeEEEEECCCCeEEEEEEecC
Confidence 468999999999999999874
No 44
>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=27.49 E-value=60 Score=19.40 Aligned_cols=18 Identities=28% Similarity=0.353 Sum_probs=15.2
Q ss_pred CHHHHHHHHHHHHHHHHH
Q 032349 76 NELAYLECIHLFVEILDH 93 (142)
Q Consensus 76 Nel~~le~l~~~v~~l~~ 93 (142)
+-+++++|++.+.++|.-
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 45
>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=27.02 E-value=1.1e+02 Score=19.72 Aligned_cols=33 Identities=18% Similarity=-0.064 Sum_probs=18.4
Q ss_pred HHHhccccHHHHHHhHHHHHHHHHHHHhCcEEe
Q 032349 92 DHFFSNVCELDLVFNFHKVYLILDEFILAGELQ 124 (142)
Q Consensus 92 ~~~f~~v~e~~i~~nf~~v~~lLDE~id~G~~~ 124 (142)
...+++..+.+.-..-.....+++.|.|+|++.
T Consensus 9 ~~~~~~~~~~~~~~~~~~~~~il~~L~d~GyI~ 41 (88)
T PF09639_consen 9 YKCMKNGKEPDPDITDSYWSDILRMLQDEGYIK 41 (88)
T ss_dssp HHH-S---HHHHTS-HHHHHHHHHHHHHHTSEE
T ss_pred HHHHcCCCCCCcchhHHHHHHHHHHHHHCCCcc
Confidence 334444433332222277788999999999984
No 46
>PRK13599 putative peroxiredoxin; Provisional
Probab=26.76 E-value=1.8e+02 Score=22.00 Aligned_cols=21 Identities=29% Similarity=0.659 Sum_probs=17.6
Q ss_pred eEEEEeecCCCCeeEEecCCC
Q 032349 2 IRFILLQNRQGKTRLAKYYVP 22 (142)
Q Consensus 2 I~~i~iln~~G~~~l~k~Y~~ 22 (142)
+.+.||+|++|+++..-+|..
T Consensus 119 ~R~tfIID~dG~Ir~~~~~p~ 139 (215)
T PRK13599 119 VRAVFIVDDKGTIRLIMYYPQ 139 (215)
T ss_pred eeEEEEECCCCEEEEEEEcCC
Confidence 468899999999999977753
No 47
>COG4114 FhuF Uncharacterized Fe-S protein [General function prediction only]
Probab=26.55 E-value=2e+02 Score=22.50 Aligned_cols=39 Identities=15% Similarity=-0.017 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHHHhccccHHHHHHh-HHHHHHHHHHHHh
Q 032349 80 YLECIHLFVEILDHFFSNVCELDLVFN-FHKVYLILDEFIL 119 (142)
Q Consensus 80 ~le~l~~~v~~l~~~f~~v~e~~i~~n-f~~v~~lLDE~id 119 (142)
+.+-|..++++|.++ |+++.+-+-+| +..++.+||||..
T Consensus 149 ~~~hL~pv~~~Lea~-g~In~rLlWnNtgyli~wyl~e~k~ 188 (251)
T COG4114 149 ISQHLVPVVQALEAT-GGINGRLLWNNTGYLINWYLTEMKQ 188 (251)
T ss_pred HHHHHHHHHHHHHHh-cCCChhhhhhhhHHHHHHHHHHHHH
Confidence 344455666666655 67888889998 7799999999983
No 48
>KOG1373 consensus Transport protein Sec61, alpha subunit [Intracellular trafficking, secretion, and vesicular transport; Posttranslational modification, protein turnover, chaperones]
Probab=26.20 E-value=1e+02 Score=26.06 Aligned_cols=49 Identities=14% Similarity=0.269 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHHHHhccccHHH----HHHhH-----HHHHHHHHHHHhCcEEeecC
Q 032349 79 AYLECIHLFVEILDHFFSNVCELD----LVFNF-----HKVYLILDEFILAGELQETS 127 (142)
Q Consensus 79 ~~le~l~~~v~~l~~~f~~v~e~~----i~~nf-----~~v~~lLDE~id~G~~~etd 127 (142)
+++.+.+.++-++..++|..++.. ++=++ -.+..+|||+++-||=+.+-
T Consensus 123 iii~vgqa~~yV~tG~yG~p~dLg~~~clLii~QL~~Agiiv~lLdEllqKGyGlgSG 180 (476)
T KOG1373|consen 123 IIITVGQAVVYVMTGMYGSPSDLGVGICLLIILQLFFAGIIVILLDELLQKGYGLGSG 180 (476)
T ss_pred HHHHHHHHHHHhhhcccCChhhcchhHHHHHHHHHHHhhHHHHHHHHHHHhccCcCcc
Confidence 455666788888889999766543 22222 35678999999999876553
No 49
>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=26.18 E-value=1.6e+02 Score=18.02 Aligned_cols=16 Identities=19% Similarity=0.291 Sum_probs=14.4
Q ss_pred eEEEEeecCCCCeeEE
Q 032349 2 IRFILLQNRQGKTRLA 17 (142)
Q Consensus 2 I~~i~iln~~G~~~l~ 17 (142)
+++.+++|++|.++-+
T Consensus 15 v~~~~l~~~dG~~i~~ 30 (91)
T PF03259_consen 15 VRGAVLVDKDGLVIAS 30 (91)
T ss_dssp EEEEEEEETTSEEEEE
T ss_pred eeEEEEEcCCCCEEEE
Confidence 6789999999999988
No 50
>PRK13191 putative peroxiredoxin; Provisional
Probab=25.56 E-value=2e+02 Score=21.66 Aligned_cols=20 Identities=30% Similarity=0.693 Sum_probs=17.4
Q ss_pred eEEEEeecCCCCeeEEecCC
Q 032349 2 IRFILLQNRQGKTRLAKYYV 21 (142)
Q Consensus 2 I~~i~iln~~G~~~l~k~Y~ 21 (142)
+.+.||+|++|.++..-+|.
T Consensus 124 ~r~tfIID~~G~Ir~~~~~~ 143 (215)
T PRK13191 124 VRAVFIVDDKGTVRLILYYP 143 (215)
T ss_pred eEEEEEECCCCEEEEEEecC
Confidence 46789999999999988886
No 51
>PF13867 SAP30_Sin3_bdg: Sin3 binding region of histone deacetylase complex subunit SAP30; PDB: 2LD7_A.
Probab=24.48 E-value=1e+02 Score=18.01 Aligned_cols=23 Identities=22% Similarity=0.384 Sum_probs=15.7
Q ss_pred HHHHHHHHHhcc--ccHHHHHHhHH
Q 032349 86 LFVEILDHFFSN--VCELDLVFNFH 108 (142)
Q Consensus 86 ~~v~~l~~~f~~--v~e~~i~~nf~ 108 (142)
.+++.+...|.+ ++|.+++-+|.
T Consensus 25 qLa~~V~kHF~s~~v~E~evI~~Fl 49 (53)
T PF13867_consen 25 QLANAVRKHFNSQPVDENEVIANFL 49 (53)
T ss_dssp HHHHHHHHHHTT----HHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHHH
Confidence 356667777765 78999998885
No 52
>PRK13189 peroxiredoxin; Provisional
Probab=24.02 E-value=2.2e+02 Score=21.54 Aligned_cols=21 Identities=24% Similarity=0.515 Sum_probs=17.2
Q ss_pred eEEEEeecCCCCeeEEecCCC
Q 032349 2 IRFILLQNRQGKTRLAKYYVP 22 (142)
Q Consensus 2 I~~i~iln~~G~~~l~k~Y~~ 22 (142)
+.+.||+|++|.++....|..
T Consensus 126 ~r~tfIID~~G~Ir~~~~~~~ 146 (222)
T PRK13189 126 VRAVFIIDPKGIIRAILYYPQ 146 (222)
T ss_pred eeEEEEECCCCeEEEEEecCC
Confidence 357899999999998887753
No 53
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) 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 homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=22.70 E-value=56 Score=20.90 Aligned_cols=40 Identities=15% Similarity=0.094 Sum_probs=27.3
Q ss_pred HHHHHHhHHHHHHHHHHHHhCcEEeecCHHHHHHHHHhhh
Q 032349 100 ELDLVFNFHKVYLILDEFILAGELQETSKRAIIERMGELE 139 (142)
Q Consensus 100 e~~i~~nf~~v~~lLDE~id~G~~~etd~~~i~~~i~~~~ 139 (142)
...++.....|-.+||-+...|++-+.+-+.|.+.-+.++
T Consensus 7 r~~Li~~v~~v~~ilD~L~~~~Vit~e~~~~I~a~~T~~~ 46 (82)
T cd08330 7 REALIARVTNVDPILDKLHGKKVITQEQYSEVRAEKTNQE 46 (82)
T ss_pred HHHHHHHHhhHHHHHHHHHHCCCCCHHHHHHHHcCCCcHH
Confidence 3456666667778888888888887777777665544443
No 54
>cd03015 PRX_Typ2cys Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides. The functional unit of typical 2-cys PRX is a homodimer. A unique intermolecular redox-active disulfide center is utilized for its activity. Upon reaction with peroxides, its peroxidatic cysteine is oxidized into a sulfenic acid intermediate which is resolved by bonding with the resolving cysteine from the other subunit of the homodimer. This intermolecular disulfide bond is then reduced by thioredoxin, tryparedoxin or AhpF. Typical 2-cys PRXs, like 1-cys PRXs, form decamers which are stabilized by reduction of the active site cysteine. Typical 2-cys PRX interacts through beta strands at one edge of the monomer (B-type interface) to form the functional homodimer, and uses an A-type interface (similar to the dimeric
Probab=22.69 E-value=2.4e+02 Score=19.95 Aligned_cols=17 Identities=18% Similarity=0.192 Sum_probs=13.2
Q ss_pred EEEEeecCCCCeeEEec
Q 032349 3 RFILLQNRQGKTRLAKY 19 (142)
Q Consensus 3 ~~i~iln~~G~~~l~k~ 19 (142)
...|++|++|.++..-.
T Consensus 121 p~~~lID~~G~I~~~~~ 137 (173)
T cd03015 121 RGTFIIDPEGIIRHITV 137 (173)
T ss_pred eEEEEECCCCeEEEEEe
Confidence 46899999998776653
No 55
>PF11411 DNA_ligase_IV: DNA ligase IV; InterPro: IPR021536 DNA ligase IV along with Xrcc4 functions in DNA non-homologous end joining. This process is required to mend double-strand breaks. Upon ligase binding to an Xrcc4 dimer, the helical tails unwind leading to a flat interaction surface []. ; GO: 0003910 DNA ligase (ATP) activity; PDB: 3II6_Y 2E2W_A 1IK9_C.
Probab=21.97 E-value=25 Score=19.28 Aligned_cols=17 Identities=18% Similarity=0.165 Sum_probs=9.9
Q ss_pred HHhccccHHHHHHhHHH
Q 032349 93 HFFSNVCELDLVFNFHK 109 (142)
Q Consensus 93 ~~f~~v~e~~i~~nf~~ 109 (142)
+|+...++..|++.|..
T Consensus 16 SY~~Dtd~~~Lk~vF~~ 32 (36)
T PF11411_consen 16 SYTVDTDEDQLKEVFNR 32 (36)
T ss_dssp BSSS---HHHHHHHHHC
T ss_pred cccccCCHHHHHHHHHH
Confidence 35556788888887764
No 56
>PRK15000 peroxidase; Provisional
Probab=21.75 E-value=2.6e+02 Score=20.71 Aligned_cols=20 Identities=20% Similarity=0.117 Sum_probs=16.7
Q ss_pred eEEEEeecCCCCeeEEecCC
Q 032349 2 IRFILLQNRQGKTRLAKYYV 21 (142)
Q Consensus 2 I~~i~iln~~G~~~l~k~Y~ 21 (142)
+.+.|++|++|.++....+.
T Consensus 125 ~r~tfiID~~G~I~~~~~~~ 144 (200)
T PRK15000 125 LRGSFLIDANGIVRHQVVND 144 (200)
T ss_pred EeEEEEECCCCEEEEEEecC
Confidence 46789999999999877664
No 57
>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional
Probab=21.45 E-value=36 Score=25.81 Aligned_cols=29 Identities=14% Similarity=0.241 Sum_probs=22.8
Q ss_pred CCeeEEecCCCCChhhHHHHHHHHHHHHh
Q 032349 12 GKTRLAKYYVPLEDSEKHKVEYEVHRLVV 40 (142)
Q Consensus 12 G~~~l~k~Y~~~~~~~~~~~~~~~~~~~~ 40 (142)
++..+.|||+..++++|+++.+.|.+.+.
T Consensus 74 s~~vLG~~wr~as~eQr~~F~~~F~~~Lv 102 (211)
T PRK15117 74 GALVLGRYYKDATPAQREAYFAAFREYLK 102 (211)
T ss_pred HHHHhhhhhhhCCHHHHHHHHHHHHHHHH
Confidence 44567789999999999999988866543
No 58
>PF07205 DUF1413: Domain of unknown function (DUF1413); InterPro: IPR010813 This family consists of several hypothetical bacterial proteins, which seem to be specific to Staphylococcus species. Members of this family are typically around 100 residues in length. The function of this family is unknown.
Probab=20.21 E-value=2.1e+02 Score=17.47 Aligned_cols=25 Identities=12% Similarity=0.074 Sum_probs=19.5
Q ss_pred cCCCCChhhHHHHHHHHHHHHhcCC
Q 032349 19 YYVPLEDSEKHKVEYEVHRLVVNRD 43 (142)
Q Consensus 19 ~Y~~~~~~~~~~~~~~~~~~~~~~~ 43 (142)
.|...+..+|+.+.+.|...+...+
T Consensus 27 ~w~~~s~~~r~~~g~~F~~~V~~~~ 51 (70)
T PF07205_consen 27 EWNTLSRAERQSLGRAFLYEVKQGP 51 (70)
T ss_pred hhhhCCHHHHHHHHHHHHHHHHhCC
Confidence 5666788888999999988886544
Done!