Query 032296
Match_columns 143
No_of_seqs 109 out of 852
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 12:13:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032296.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032296hhsearch_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 6.7E-44 1.5E-48 257.9 18.9 141 2-142 1-141 (141)
2 COG5030 APS2 Clathrin adaptor 100.0 2.9E-42 6.3E-47 244.6 14.3 141 2-142 1-141 (152)
3 KOG0936 Clathrin adaptor compl 100.0 8.4E-39 1.8E-43 230.2 14.0 142 2-143 1-148 (182)
4 KOG0934 Clathrin adaptor compl 100.0 5.9E-39 1.3E-43 227.2 8.7 141 2-142 1-141 (145)
5 KOG0935 Clathrin adaptor compl 100.0 5.2E-37 1.1E-41 213.2 11.6 142 2-143 1-143 (143)
6 KOG3343 Vesicle coat complex C 100.0 2.1E-32 4.6E-37 198.2 12.5 136 2-140 8-147 (175)
7 KOG0938 Adaptor complexes medi 100.0 2.5E-29 5.5E-34 201.2 12.9 134 2-139 1-135 (446)
8 KOG0937 Adaptor complexes medi 99.9 1.9E-23 4.1E-28 172.1 14.0 135 3-139 1-136 (424)
9 COG5541 RET3 Vesicle coat comp 99.9 3E-23 6.5E-28 150.3 9.8 134 2-138 7-152 (187)
10 KOG2740 Clathrin-associated pr 99.9 1.5E-23 3.3E-28 169.0 8.6 135 2-138 1-137 (418)
11 KOG2635 Medium subunit of clat 99.2 6.5E-10 1.4E-14 92.4 12.5 136 1-138 1-136 (512)
12 PF15001 AP-5_subunit_s1: AP-5 97.6 0.0095 2.1E-07 45.2 14.8 80 54-133 102-182 (189)
13 PF03164 Mon1: Trafficking pro 97.2 0.017 3.7E-07 48.7 13.6 90 4-96 12-103 (415)
14 PF08923 MAPKK1_Int: Mitogen-a 95.6 0.18 4E-06 35.5 9.0 92 3-95 17-115 (119)
15 PF04099 Sybindin: Sybindin-li 95.1 0.84 1.8E-05 32.9 12.4 93 3-96 1-115 (142)
16 COG5122 TRS23 Transport protei 94.8 0.62 1.3E-05 32.7 9.4 93 1-96 1-106 (134)
17 PF13774 Longin: Regulated-SNA 91.3 2.5 5.4E-05 27.2 7.8 48 50-97 18-65 (83)
18 KOG3369 Transport protein part 91.3 5.2 0.00011 30.2 10.3 46 49-96 124-170 (199)
19 KOG0997 Uncharacterized conser 90.3 4.8 0.0001 34.9 10.5 78 5-83 119-196 (523)
20 KOG0862 Synaptobrevin/VAMP-lik 89.1 9.1 0.0002 29.7 11.5 94 4-98 4-101 (216)
21 KOG0859 Synaptobrevin/VAMP-lik 84.6 16 0.00036 28.1 10.1 87 7-97 5-92 (217)
22 KOG3368 Transport protein part 81.4 18 0.00038 26.1 11.3 88 1-90 1-102 (140)
23 PF09201 SRX: SRX; InterPro: 79.7 21 0.00046 26.0 8.2 73 2-74 1-86 (148)
24 PF04086 SRP-alpha_N: Signal r 68.6 56 0.0012 25.7 8.9 49 50-98 21-71 (279)
25 PF08006 DUF1700: Protein of u 63.3 18 0.00038 26.7 4.7 51 88-138 6-62 (181)
26 PF03259 Robl_LC7: Roadblock/L 56.1 48 0.001 20.8 7.4 62 3-67 15-85 (91)
27 PF05228 CHASE4: CHASE4 domain 55.6 47 0.001 23.3 5.7 21 3-23 50-72 (161)
28 COG3322 Predicted periplasmic 55.3 11 0.00023 30.7 2.5 21 3-23 104-124 (295)
29 PF08217 DUF1712: Fungal domai 54.4 1.3E+02 0.0028 26.9 9.3 73 45-119 55-135 (604)
30 KOG0861 SNARE protein YKT6, sy 52.1 1E+02 0.0022 23.4 8.2 91 1-92 1-101 (198)
31 KOG0781 Signal recognition par 51.2 1.8E+02 0.0038 25.8 10.9 111 2-116 1-115 (587)
32 PF02334 RTP: Replication term 50.1 29 0.00063 24.3 3.6 34 88-124 37-70 (122)
33 PF08784 RPA_C: Replication pr 46.2 21 0.00045 23.7 2.5 46 83-128 47-99 (102)
34 PF01535 PPR: PPR repeat; Int 43.2 23 0.00049 17.3 1.8 18 106-123 14-31 (31)
35 PF13812 PPR_3: Pentatricopept 37.5 29 0.00064 17.3 1.7 18 106-123 15-32 (34)
36 KOG1373 Transport protein Sec6 37.0 53 0.0012 28.0 3.9 50 80-129 123-181 (476)
37 PF02268 TFIIA_gamma_N: Transc 34.7 38 0.00083 20.1 2.0 15 111-125 15-29 (49)
38 PF14903 WG_beta_rep: WG conta 32.3 54 0.0012 16.8 2.3 17 8-24 3-19 (35)
39 KOG0903 Phosphatidylinositol 4 31.8 2.7E+02 0.0058 26.0 7.6 93 28-123 679-788 (847)
40 cd08324 CARD_NOD1_CARD4 Caspas 31.3 35 0.00076 22.6 1.6 42 101-142 7-48 (85)
41 PF15047 DUF4533: Protein of u 30.6 90 0.002 24.4 4.0 38 81-118 19-63 (225)
42 COG1049 AcnB Aconitase B [Ener 30.0 76 0.0016 28.8 3.9 41 98-141 601-641 (852)
43 TIGR00756 PPR pentatricopeptid 29.8 44 0.00096 16.4 1.6 20 106-125 14-33 (35)
44 KOG4281 Uncharacterized conser 27.3 70 0.0015 25.0 2.9 36 84-119 3-38 (236)
45 PF13041 PPR_2: PPR repeat fam 26.9 46 0.001 18.7 1.5 23 106-128 17-39 (50)
46 PRK05483 rplN 50S ribosomal pr 26.0 87 0.0019 22.1 3.0 26 4-29 82-107 (122)
47 PF09639 YjcQ: YjcQ protein; 25.5 1.4E+02 0.003 19.5 3.7 17 109-125 25-41 (88)
48 cd08330 CARD_ASC_NALP1 Caspase 25.1 42 0.0009 21.7 1.2 40 102-141 8-47 (82)
49 PF13337 Lon_2: Putative ATP-d 25.1 1.3E+02 0.0027 26.2 4.3 55 77-141 23-77 (457)
50 COG0450 AhpC Peroxiredoxin [Po 25.1 3E+02 0.0065 21.1 6.0 22 2-23 123-144 (194)
51 TIGR01067 rplN_bact ribosomal 24.3 96 0.0021 21.8 3.0 26 4-29 82-107 (122)
52 PF09561 RE_HpaII: HpaII restr 24.1 3.1E+02 0.0068 23.0 6.3 56 3-68 292-347 (355)
53 PF00741 Gas_vesicle: Gas vesi 23.2 71 0.0015 18.0 1.7 18 111-128 2-19 (39)
54 PRK15360 pathogenicity island 22.5 3.1E+02 0.0066 19.8 7.1 50 50-103 30-83 (137)
55 CHL00057 rpl14 ribosomal prote 21.5 1.2E+02 0.0025 21.4 2.9 25 4-28 82-106 (122)
56 cd04685 Nudix_Hydrolase_26 Mem 20.6 1.1E+02 0.0025 21.2 2.8 19 4-22 3-21 (133)
57 cd03671 Ap4A_hydrolase_plant_l 20.5 1.1E+02 0.0024 21.3 2.8 19 4-22 6-24 (147)
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=6.7e-44 Score=257.92 Aligned_cols=141 Identities=40% Similarity=0.676 Sum_probs=131.1
Q ss_pred ceEEEEEEeCCCCEEEEecCcCCCHHHHHHHHHHHHHHHhcccCCCcceeEeCCEEEEEEEeCcEEEEEEEcCCcCHHHH
Q 032296 2 GIRFILMVNKQGQTRLAQYYEWLTLEERRALEGEIVRKCLARTEQQCSFVEHRNYKIVYRRYASLFFLVGVDNDENELAI 81 (143)
Q Consensus 2 mI~~~~iln~~G~~il~k~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~f~~~~~~~~nel~~ 81 (143)
||+|++|+|++|+++++|||++.+.++++++.+++.+.+.++++..+|++.++++++||+++++|||+++++.++||+++
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 99999999999999999999988777778888888888777777789999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhccccHHHHHhhHHHHHHHHHHHHhCcEEeecCHHHHHHHHhhhhcc
Q 032296 82 LEFIHLLVETMDRHFGNVCELDIMFHLEKAHFMLEEMVMNGCIVETSKSNILSPIQLMEKM 142 (143)
Q Consensus 82 ~e~L~~~v~~l~~~f~~v~e~~i~~nf~~vy~iLDEiid~G~~~eT~~~~i~~~i~~~~~~ 142 (143)
+++|++++++|+.|||++||+++++||+++|++||||+|+|+|+|||++.|++|++++|++
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 9999999999999999999999999999999999999999999999999999999999974
No 2
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=100.00 E-value=2.9e-42 Score=244.57 Aligned_cols=141 Identities=45% Similarity=0.800 Sum_probs=137.0
Q ss_pred ceEEEEEEeCCCCEEEEecCcCCCHHHHHHHHHHHHHHHhcccCCCcceeEeCCEEEEEEEeCcEEEEEEEcCCcCHHHH
Q 032296 2 GIRFILMVNKQGQTRLAQYYEWLTLEERRALEGEIVRKCLARTEQQCSFVEHRNYKIVYRRYASLFFLVGVDNDENELAI 81 (143)
Q Consensus 2 mI~~~~iln~~G~~il~k~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~f~~~~~~~~nel~~ 81 (143)
||++++|+|++|++||.|||.+.+.++|.++.+++++.+++|++++|++.+..+.++|||||++|||+++++.++||+++
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 HHHHHHHHHHHHhhhccccHHHHHhhHHHHHHHHHHHHhCcEEeecCHHHHHHHHhhhhcc
Q 032296 82 LEFIHLLVETMDRHFGNVCELDIMFHLEKAHFMLEEMVMNGCIVETSKSNILSPIQLMEKM 142 (143)
Q Consensus 82 ~e~L~~~v~~l~~~f~~v~e~~i~~nf~~vy~iLDEiid~G~~~eT~~~~i~~~i~~~~~~ 142 (143)
++++|.|+++|+.|||++||.++++||.++|.+||||+.+|.++||++..+++++...|++
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=8.4e-39 Score=230.17 Aligned_cols=142 Identities=36% Similarity=0.717 Sum_probs=136.6
Q ss_pred ceEEEEEEeCCCCEEEEecCcCCCHHHHHHHHHHHHHHHhcccCCCcceeEe------CCEEEEEEEeCcEEEEEEEcCC
Q 032296 2 GIRFILMVNKQGQTRLAQYYEWLTLEERRALEGEIVRKCLARTEQQCSFVEH------RNYKIVYRRYASLFFLVGVDND 75 (143)
Q Consensus 2 mI~~~~iln~~G~~il~k~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~------~~~~~vy~~~~~l~f~~~~~~~ 75 (143)
||+|++|+|++|++|+.|||++.+.+.|+++.+++|..+++|++..|++++. .+.+++||+|+.|||+.++|+.
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 8999999999999999999999999999999999999999999999999863 3789999999999999999999
Q ss_pred cCHHHHHHHHHHHHHHHHhhhccccHHHHHhhHHHHHHHHHHHHhCcEEeecCHHHHHHHHhhhhccC
Q 032296 76 ENELAILEFIHLLVETMDRHFGNVCELDIMFHLEKAHFMLEEMVMNGCIVETSKSNILSPIQLMEKMS 143 (143)
Q Consensus 76 ~nel~~~e~L~~~v~~l~~~f~~v~e~~i~~nf~~vy~iLDEiid~G~~~eT~~~~i~~~i~~~~~~~ 143 (143)
|+||.+++++|.||++|+++|.++||.|+++|+++++.+|+|++.+|.++||+.+.|...+..|.+++
T Consensus 81 EsEL~iLDLIQvfVEtLDkCF~nVcELDliF~~~k~h~iL~EiV~GGmVlETn~neIv~av~~~nkle 148 (182)
T KOG0936|consen 81 ESELGILDLIQVFVETLDKCFENVCELDLIFNWQKVHAILAEIVMGGMVLETNMNEIVAAVDEQNKLE 148 (182)
T ss_pred cchhHHHHHHHHHHHHHHHHHHhhhhhhheeeHHHHHHHHHHHHhCCeEEeccHHHHHHHHHHhchhh
Confidence 99999999999999999999999999999999999999999999999999999999999999988763
No 4
>KOG0934 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=5.9e-39 Score=227.20 Aligned_cols=141 Identities=52% Similarity=0.930 Sum_probs=137.4
Q ss_pred ceEEEEEEeCCCCEEEEecCcCCCHHHHHHHHHHHHHHHhcccCCCcceeEeCCEEEEEEEeCcEEEEEEEcCCcCHHHH
Q 032296 2 GIRFILMVNKQGQTRLAQYYEWLTLEERRALEGEIVRKCLARTEQQCSFVEHRNYKIVYRRYASLFFLVGVDNDENELAI 81 (143)
Q Consensus 2 mI~~~~iln~~G~~il~k~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~f~~~~~~~~nel~~ 81 (143)
||+++++.|++|+++|+|||.+.+.++|++.++++.+.+++|+++.|++++++++++|||||++|||+++...++|||++
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 HHHHHHHHHHHHhhhccccHHHHHhhHHHHHHHHHHHHhCcEEeecCHHHHHHHHhhhhcc
Q 032296 82 LEFIHLLVETMDRHFGNVCELDIMFHLEKAHFMLEEMVMNGCIVETSKSNILSPIQLMEKM 142 (143)
Q Consensus 82 ~e~L~~~v~~l~~~f~~v~e~~i~~nf~~vy~iLDEiid~G~~~eT~~~~i~~~i~~~~~~ 142 (143)
+|++|+++++|+.|||+|||.|+++||.++|.+|||.+-+|-++||+.+...+.++++|-+
T Consensus 81 LE~IH~~vE~lDkYFg~VCELDiiFNfekay~ILde~~~~g~~~e~~k~~~~~~i~~ad~l 141 (145)
T KOG0934|consen 81 LEFIHNYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEIQETSKNDVLKAIAQADLL 141 (145)
T ss_pred HHHHHHHHHHHHHHhccceeeEEEEehHhHHHHHHHHhcCcchHhhhcccHHHHHHHhhhc
Confidence 9999999999999999999999999999999999999999999999999999999888754
No 5
>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=5.2e-37 Score=213.17 Aligned_cols=142 Identities=44% Similarity=0.748 Sum_probs=131.9
Q ss_pred ceEEEEEEeCCCCEEEEecCcCCCHHHHHHHHHHHHHHHhcccCCCcceeEeCCEEEEE-EEeCcEEEEEEEcCCcCHHH
Q 032296 2 GIRFILMVNKQGQTRLAQYYEWLTLEERRALEGEIVRKCLARTEQQCSFVEHRNYKIVY-RRYASLFFLVGVDNDENELA 80 (143)
Q Consensus 2 mI~~~~iln~~G~~il~k~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy-~~~~~l~f~~~~~~~~nel~ 80 (143)
||++++|.|++|+++++|||-+.+++++.+.+.++++.+..|+.+..++++..+.+++| |||++|||+.+++.-+||++
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 89999999999999999999988777788899999999988887777767666666555 59999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhccccHHHHHhhHHHHHHHHHHHHhCcEEeecCHHHHHHHHhhhhccC
Q 032296 81 ILEFIHLLVETMDRHFGNVCELDIMFHLEKAHFMLEEMVMNGCIVETSKSNILSPIQLMEKMS 143 (143)
Q Consensus 81 ~~e~L~~~v~~l~~~f~~v~e~~i~~nf~~vy~iLDEiid~G~~~eT~~~~i~~~i~~~~~~~ 143 (143)
.++-+|.||++|++||||+||.++.+||-+||.++|||+-+|.++||++..+++|+.+.++++
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 999999999999999999999999999999999999999999999999999999999999874
No 6
>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=2.1e-32 Score=198.15 Aligned_cols=136 Identities=24% Similarity=0.427 Sum_probs=126.3
Q ss_pred ceEEEEEEeCCCCEEEEecCcC--CC-HHHHHHHHHHHHHHHhcccCCCcceeEeCCEEEEEEEeCcEEEEEEEcCCcCH
Q 032296 2 GIRFILMVNKQGQTRLAQYYEW--LT-LEERRALEGEIVRKCLARTEQQCSFVEHRNYKIVYRRYASLFFLVGVDNDENE 78 (143)
Q Consensus 2 mI~~~~iln~~G~~il~k~Y~~--~~-~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~f~~~~~~~~ne 78 (143)
.++|++|+|++|+|+++|||.+ ++ -++|+.||+.+|+++.+ ....|..++|..+||+..-||+|++++..+|||
T Consensus 8 ~vk~iliLD~~G~Ri~aKYY~~~~~s~vkeqkaFEK~lF~KT~k---t~~eI~~ldg~~vvYk~~~Dl~fyv~G~~~ENE 84 (175)
T KOG3343|consen 8 TVKAILILDSDGKRILAKYYDDPHPSTVKEQKAFEKNLFSKTSK---TESEILLLDGNTVVYKSVIDLHFYVVGSEEENE 84 (175)
T ss_pred hhheEEEEcCCCCEeeeeecCCCcchhHHHHHHHHHHHhccccc---ccceeEEecCcEEEEEecccEEEEEecCcchhH
Confidence 4789999999999999999985 33 67999999999999865 356788899999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhc-cccHHHHHhhHHHHHHHHHHHHhCcEEeecCHHHHHHHHhhhh
Q 032296 79 LAILEFIHLLVETMDRHFG-NVCELDIMFHLEKAHFMLEEMVMNGCIVETSKSNILSPIQLME 140 (143)
Q Consensus 79 l~~~e~L~~~v~~l~~~f~-~v~e~~i~~nf~~vy~iLDEiid~G~~~eT~~~~i~~~i~~~~ 140 (143)
+++.++|+++.+++...++ ++.+..+++|++.+.+.+||++|+|.++||||+.|+.|++...
T Consensus 85 l~L~svL~~l~dal~llLr~nveKr~llEN~D~i~L~~DEiiD~GvILEtdp~~ia~rv~~~~ 147 (175)
T KOG3343|consen 85 LMLMSVLTCLFDALSLLLRKNVEKRELLENLDLIFLALDEIIDGGVILETDPNQIAQRVALRP 147 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHhChhHHHHHhhhccceeehhhhccCceEEecCHHHHHHHhccCC
Confidence 9999999999999999996 7999999999999999999999999999999999999998653
No 7
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.96 E-value=2.5e-29 Score=201.24 Aligned_cols=134 Identities=17% Similarity=0.170 Sum_probs=124.0
Q ss_pred ceEEEEEEeCCCCEEEEecCcCCCHHHHHHHHHHHHHH-HhcccCCCcceeEeCCEEEEEEEeCcEEEEEEEcCCcCHHH
Q 032296 2 GIRFILMVNKQGQTRLAQYYEWLTLEERRALEGEIVRK-CLARTEQQCSFVEHRNYKIVYRRYASLFFLVGVDNDENELA 80 (143)
Q Consensus 2 mI~~~~iln~~G~~il~k~Y~~~~~~~~~~~~~~~~~~-~~~~~~~~~~i~~~~~~~~vy~~~~~l~f~~~~~~~~nel~ 80 (143)
||+++||+|.+|++++.|.||.. -++-.-++||. ++......||++.+++++++|.|..+||+++++++|.|..+
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 89999999999999999999973 23446778885 66555678999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhccccHHHHHhhHHHHHHHHHHHHhCcEEeecCHHHHHHHHhhh
Q 032296 81 ILEFIHLLVETMDRHFGNVCELDIMFHLEKAHFMLEEMVMNGCIVETSKSNILSPIQLM 139 (143)
Q Consensus 81 ~~e~L~~~v~~l~~~f~~v~e~~i~~nf~~vy~iLDEiid~G~~~eT~~~~i~~~i~~~ 139 (143)
++|||..+.+++.+|||..+|+.+++||..+|++||||+|+||||+|+|+.++..++++
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 99999999999999999999999999999999999999999999999999999998865
No 8
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.91 E-value=1.9e-23 Score=172.09 Aligned_cols=135 Identities=12% Similarity=0.219 Sum_probs=118.3
Q ss_pred eEEEEEEeCCCCEEEEecCcC-CCHHHHHHHHHHHHHHHhcccCCCcceeEeCCEEEEEEEeCcEEEEEEEcCCcCHHHH
Q 032296 3 IRFILMVNKQGQTRLAQYYEW-LTLEERRALEGEIVRKCLARTEQQCSFVEHRNYKIVYRRYASLFFLVGVDNDENELAI 81 (143)
Q Consensus 3 I~~~~iln~~G~~il~k~Y~~-~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~f~~~~~~~~nel~~ 81 (143)
++|+|++|.+|+++++|.||. .+.....+|..-++.+. ..+...|++.++|..++|.++++||++++++.|.|+..+
T Consensus 1 ~sa~fild~~G~~lisr~yr~dv~~s~~~~F~~~l~~~e--~~~~~~p~l~~~g~~~~~ik~s~lylv~~~~~n~~a~~v 78 (424)
T KOG0937|consen 1 ASAVFILDHKGEVLISRDYRGDVPMSSTEKFFRKLFEKE--EGDESPPFLVHDGSRFIHIKHSNLYLVAGTRPNVSAALV 78 (424)
T ss_pred CceEEEEcCCCcEeEeecccccCChhhhhhHHHHHhhhc--ccCCCCCeEEeCCceEEEEeecceEEEEEeccCCCHHHH
Confidence 579999999999999999996 33444444543222222 234578999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhccccHHHHHhhHHHHHHHHHHHHhCcEEeecCHHHHHHHHhhh
Q 032296 82 LEFIHLLVETMDRHFGNVCELDIMFHLEKAHFMLEEMVMNGCIVETSKSNILSPIQLM 139 (143)
Q Consensus 82 ~e~L~~~v~~l~~~f~~v~e~~i~~nf~~vy~iLDEiid~G~~~eT~~~~i~~~i~~~ 139 (143)
+++|+++++++.+||+.+.|..+++||+++|++|||++|+||||+|+++.+.+.+++.
T Consensus 79 ~~~l~~~~~v~~~y~~~l~e~si~~n~vlvyElLde~mDFGypQ~t~s~iL~~yi~~~ 136 (424)
T KOG0937|consen 79 LSFLYAVADVFGDYLSELEEESIRDNFVLVYELLDEVMDFGYPQTTDSEILKNYITQK 136 (424)
T ss_pred HHHHHHHHHHHHHHhccCCccceecchHHHHHHHHHHhccCCcccchHHHHHHHhccc
Confidence 9999999999999999999999999999999999999999999999999999998876
No 9
>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=99.90 E-value=3e-23 Score=150.32 Aligned_cols=134 Identities=13% Similarity=0.253 Sum_probs=122.6
Q ss_pred ceEEEEEEeCCCCEEEEecCcCC-----------CHHHHHHHHHHHHHHHhcccCCCcceeEeCCEEEEEEEeCcEEEEE
Q 032296 2 GIRFILMVNKQGQTRLAQYYEWL-----------TLEERRALEGEIVRKCLARTEQQCSFVEHRNYKIVYRRYASLFFLV 70 (143)
Q Consensus 2 mI~~~~iln~~G~~il~k~Y~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~f~~ 70 (143)
.+.|++|+|++|+|++.|||.|+ +-++++.|++.+++++.+. ...|+.+++..++|+++.|+.|+.
T Consensus 7 ~v~a~LilDsqGeriy~kyy~pph~~eg~~~vFnsvkkekefek~l~eKt~k~---~~~Il~f~d~lV~~k~~~dv~~yi 83 (187)
T COG5541 7 DVEALLILDSQGERIYRKYYQPPHRSEGHQLVFNSVKKEKEFEKKLAEKTAKD---RESILMFYDRLVMCKRLDDVLLYI 83 (187)
T ss_pred eeeeeEEecCCccchhhhhcCCcccccccchhhcchhHHHHHHHHHHHHhhcC---ccceeeEcceeeeeeeehhEEEEE
Confidence 47899999999999999999973 4467899999999998653 456788999999999999999999
Q ss_pred EEcCCcCHHHHHHHHHHHHHHHHhhhccc-cHHHHHhhHHHHHHHHHHHHhCcEEeecCHHHHHHHHhh
Q 032296 71 GVDNDENELAILEFIHLLVETMDRHFGNV-CELDIMFHLEKAHFMLEEMVMNGCIVETSKSNILSPIQL 138 (143)
Q Consensus 71 ~~~~~~nel~~~e~L~~~v~~l~~~f~~v-~e~~i~~nf~~vy~iLDEiid~G~~~eT~~~~i~~~i~~ 138 (143)
++.-++||.++.+.+..+-++|.-.++.. ++..+.+|++.+..++||.+|+|.++||+++.|++|++.
T Consensus 84 v~~meeNE~~l~q~f~~ir~Al~li~k~~~dkr~v~enYDqivl~vdEtid~Gvilet~s~~ia~rv~K 152 (187)
T COG5541 84 VSPMEENEPFLGQVFDEIRAALILIVKTPTDKRNVWENYDQIVLLVDETIDEGVILETKSDEIADRVPK 152 (187)
T ss_pred ecccccccHHHHHHHHHHHHHHHHHHcCCcchhhHHhhhceEEEeeehhcccceEeecChHHHHHhCCC
Confidence 99999999999999999999999999864 677799999999999999999999999999999999875
No 10
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.89 E-value=1.5e-23 Score=168.99 Aligned_cols=135 Identities=19% Similarity=0.206 Sum_probs=114.5
Q ss_pred ceEEEEEEeCCCCEEEEecCcCCCHHHHHHHHHHHHHHHhc--ccCCCcceeEeCCEEEEEEEeCcEEEEEEEcCCcCHH
Q 032296 2 GIRFILMVNKQGQTRLAQYYEWLTLEERRALEGEIVRKCLA--RTEQQCSFVEHRNYKIVYRRYASLFFLVGVDNDENEL 79 (143)
Q Consensus 2 mI~~~~iln~~G~~il~k~Y~~~~~~~~~~~~~~~~~~~~~--~~~~~~~i~~~~~~~~vy~~~~~l~f~~~~~~~~nel 79 (143)
||+++|+.|.+|+.+++|.+++... -+..+..+|+.-.+ +.++.+|+...+.+.++-.-..+++|++++..+..||
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 8999999999999999999995211 13445555554322 4456777777777777665566899999999999999
Q ss_pred HHHHHHHHHHHHHHhhhccccHHHHHhhHHHHHHHHHHHHhCcEEeecCHHHHHHHHhh
Q 032296 80 AILEFIHLLVETMDRHFGNVCELDIMFHLEKAHFMLEEMVMNGCIVETSKSNILSPIQL 138 (143)
Q Consensus 80 ~~~e~L~~~v~~l~~~f~~v~e~~i~~nf~~vy~iLDEiid~G~~~eT~~~~i~~~i~~ 138 (143)
++.|||+|+++++..|||+++|..|++|++.||++||||+|+|+|..|+|+.|++.|+.
T Consensus 79 ~~iefL~rv~dv~~eyFg~~s~~~Ik~N~~vv~ell~emiDnGfpl~tE~NiLke~i~p 137 (418)
T KOG2740|consen 79 MVIEFLHRVVDVLLEYFGGLSESKIKDNVVVVYELLDEMIDNGFPLVTEPNILKELIPP 137 (418)
T ss_pred hHHHHHHHHHHHHHHHhcccCHhHhhcceeeHHHHHHHHHHcCCCcccChhHHHhhcCC
Confidence 99999999999999999999999999999999999999999999999999999987753
No 11
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.16 E-value=6.5e-10 Score=92.44 Aligned_cols=136 Identities=17% Similarity=0.241 Sum_probs=120.1
Q ss_pred CceEEEEEEeCCCCEEEEecCcCCCHHHHHHHHHHHHHHHhcccCCCcceeEeCCEEEEEEEeCcEEEEEEEcCCcCHHH
Q 032296 1 MGIRFILMVNKQGQTRLAQYYEWLTLEERRALEGEIVRKCLARTEQQCSFVEHRNYKIVYRRYASLFFLVGVDNDENELA 80 (143)
Q Consensus 1 mmI~~~~iln~~G~~il~k~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~f~~~~~~~~nel~ 80 (143)
||+-|.-+.+..|+.+++|.|+.++..+-..+..++...+. ...+.-+++.+..++||....++|++.++..+.|-+-
T Consensus 1 Mvvlaa~i~t~~Gk~ivsRqf~~Msr~RIEgLl~aFpkLv~--~~~qhT~vEt~~VRYVYqP~d~lY~vLITtk~SNIle 78 (512)
T KOG2635|consen 1 MVVLAASINTKTGKAIVSRQFREMSRSRIEGLLAAFPKLVS--AGKQHTFVETDSVRYVYQPLDNLYIVLITTKQSNILE 78 (512)
T ss_pred CeEEEEEEeecCCceeeehHhHhhhHHHHHHHHHHhHHhhc--cCCCccEEecccEEEEEEecccEEEEEEeccccchhh
Confidence 89999999999999999999999887766666666544443 2245678999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhccccHHHHHhhHHHHHHHHHHHHhCcEEeecCHHHHHHHHhh
Q 032296 81 ILEFIHLLVETMDRHFGNVCELDIMFHLEKAHFMLEEMVMNGCIVETSKSNILSPIQL 138 (143)
Q Consensus 81 ~~e~L~~~v~~l~~~f~~v~e~~i~~nf~~vy~iLDEiid~G~~~eT~~~~i~~~i~~ 138 (143)
-++.|+.|..+...|+..+.|+.|.+|---+...+||++--||-...+-..|+..+.|
T Consensus 79 Dl~TL~Lfskvipey~~slde~eI~~~~FelifAFDEivsLGyre~v~laQikty~eM 136 (512)
T KOG2635|consen 79 DLETLRLFSKVIPEYCSSLDEKEILENAFELIFAFDEIVSLGYRENVNLAQIKTYLEM 136 (512)
T ss_pred HHHHHHHHHHhchhhhhhhhHHHHHHhhhhhhhccchhhhhcccccccHHHhhhhhcc
Confidence 9999999999999999999999999999999999999999999888888777776654
No 12
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=97.55 E-value=0.0095 Score=45.23 Aligned_cols=80 Identities=14% Similarity=0.244 Sum_probs=70.2
Q ss_pred CCEEEEEEEeCcEEEEEEEcCCcCHHHHHHHHHHHHHHHHhhhccccH-HHHHhhHHHHHHHHHHHHhCcEEeecCHHHH
Q 032296 54 RNYKIVYRRYASLFFLVGVDNDENELAILEFIHLLVETMDRHFGNVCE-LDIMFHLEKAHFMLEEMVMNGCIVETSKSNI 132 (143)
Q Consensus 54 ~~~~~vy~~~~~l~f~~~~~~~~nel~~~e~L~~~v~~l~~~f~~v~e-~~i~~nf~~vy~iLDEiid~G~~~eT~~~~i 132 (143)
+...++|+...++-|..+++..||-+.+-.+|..++..+.+.++.++. ..+..+-+.|..+|+..+=.|-.+=-+.+.+
T Consensus 102 ~~k~vvW~~v~~l~ftLVce~hEN~lLa~~~L~~~~~~l~~~~~~l~~~~e~l~k~d~i~aiL~~fLP~GQLLFlN~~~~ 181 (189)
T PF15001_consen 102 TPKIVVWLGVGSLCFTLVCEPHENRLLAENTLRLFIRHLLEHLKILSQPSEVLLKSDRILAILHRFLPHGQLLFLNHRFV 181 (189)
T ss_pred CCcEEEeeccCCEEEEEEecCchhHHHHHHHHHHHHHHHHHHHHHhCcHHHhhhhHHHHHHHHHHhCCCCcEEEEcHHHH
Confidence 346788999999999999999999999999999999999999976544 6677799999999999999998887777665
Q ss_pred H
Q 032296 133 L 133 (143)
Q Consensus 133 ~ 133 (143)
+
T Consensus 182 k 182 (189)
T PF15001_consen 182 K 182 (189)
T ss_pred H
Confidence 4
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=97.16 E-value=0.017 Score=48.71 Aligned_cols=90 Identities=12% Similarity=0.187 Sum_probs=61.7
Q ss_pred EEEEEEeCCCCEEEEecCcCCCHHHHHHHHHHHHHHHhc--ccCCCcceeEeCCEEEEEEEeCcEEEEEEEcCCcCHHHH
Q 032296 4 RFILMVNKQGQTRLAQYYEWLTLEERRALEGEIVRKCLA--RTEQQCSFVEHRNYKIVYRRYASLFFLVGVDNDENELAI 81 (143)
Q Consensus 4 ~~~~iln~~G~~il~k~Y~~~~~~~~~~~~~~~~~~~~~--~~~~~~~i~~~~~~~~vy~~~~~l~f~~~~~~~~nel~~ 81 (143)
+-+||+++.||++++|| .+++.-..+..-+...+.. ..++.---+..+++++|+...+.|+++++++.+|++..+
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---GDEDKLSSLMGVIQAIISFFQSNGDELRSIRAGDHRIVFLNRGPLILVAVSKTGESESQL 88 (415)
T ss_pred CeEEEECCCCceeEEec---CChHHHHHHHHHHHHHHHHHHhCCCcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCHHHH
Confidence 46899999999999999 2233333333333222221 111222234568999999999999999999999998888
Q ss_pred HHHHHHHHHHHHhhh
Q 032296 82 LEFIHLLVETMDRHF 96 (143)
Q Consensus 82 ~e~L~~~v~~l~~~f 96 (143)
..-|+.+...+-..+
T Consensus 89 ~~qL~~ly~qils~l 103 (415)
T PF03164_consen 89 RKQLDYLYSQILSIL 103 (415)
T ss_pred HHHHHHHHHHHHHhc
Confidence 877777666655554
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=95.62 E-value=0.18 Score=35.51 Aligned_cols=92 Identities=12% Similarity=0.108 Sum_probs=61.4
Q ss_pred eEEEEEEeCCCCEEEEecCcCCCH-HHHHHHHHHHHHH----Hhcc--cCCCcceeEeCCEEEEEEEeCcEEEEEEEcCC
Q 032296 3 IRFILMVNKQGQTRLAQYYEWLTL-EERRALEGEIVRK----CLAR--TEQQCSFVEHRNYKIVYRRYASLFFLVGVDND 75 (143)
Q Consensus 3 I~~~~iln~~G~~il~k~Y~~~~~-~~~~~~~~~~~~~----~~~~--~~~~~~i~~~~~~~~vy~~~~~l~f~~~~~~~ 75 (143)
+.+++|-|++|=+++.=.....+. .-+..+... |.. +.+- +.+..-+..++++.+++.....+++.++++.+
T Consensus 17 l~~I~itDrDGvpi~~v~~~~~~~~~~~~~~~~t-f~~a~~Q~~KL~lG~nk~ii~~Y~~~qvv~~~~~pl~it~ias~~ 95 (119)
T PF08923_consen 17 LQAIVITDRDGVPIAKVSSDSAPESAMRPSLLST-FAMAIDQASKLGLGKNKSIIAYYDSYQVVQFNKLPLYITFIASSN 95 (119)
T ss_dssp EEEEEEEETTS-EEEEEE-TTS-GGGGSHHHHCC-HHHHHHHHTTSSS-SEEEEEEEESSEEEEEEEETTEEEEEEEETT
T ss_pred eEEEEEECCCCcEEEEecCCCCcchhhhhHHHHH-HHHHhhcccccCCCCceEEEEEeCCEEEEEEeCCCeEEEEEecCC
Confidence 679999999999988755554322 111222222 222 2111 12334466789999999999999999999999
Q ss_pred cCHHHHHHHHHHHHHHHHhh
Q 032296 76 ENELAILEFIHLLVETMDRH 95 (143)
Q Consensus 76 ~nel~~~e~L~~~v~~l~~~ 95 (143)
.|--.++++-+.+.+.+...
T Consensus 96 aN~G~il~l~~~L~~~l~~l 115 (119)
T PF08923_consen 96 ANTGLILSLEEELAPILNEL 115 (119)
T ss_dssp S-HHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHhHHHHHHHHHHH
Confidence 99999999888887777643
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=95.12 E-value=0.84 Score=32.92 Aligned_cols=93 Identities=15% Similarity=0.162 Sum_probs=55.5
Q ss_pred eEEEEEEeCCCCEEEEecCcCC--------CHHHHHHHHHHHHHH--H-hcccC--------CCc--ceeEeCCEEE-EE
Q 032296 3 IRFILMVNKQGQTRLAQYYEWL--------TLEERRALEGEIVRK--C-LARTE--------QQC--SFVEHRNYKI-VY 60 (143)
Q Consensus 3 I~~~~iln~~G~~il~k~Y~~~--------~~~~~~~~~~~~~~~--~-~~~~~--------~~~--~i~~~~~~~~-vy 60 (143)
|.+++|+|+.|.-+..|-|... +..+++.+..-++.. + .+-++ ..+ .-++.+.+++ .|
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 6899999999999999999853 234454544444432 1 11111 112 2345577776 45
Q ss_pred EEeCcEEEEEEEcCCcCHHHHHHHHHHHHHHHHhhh
Q 032296 61 RRYASLFFLVGVDNDENELAILEFIHLLVETMDRHF 96 (143)
Q Consensus 61 ~~~~~l~f~~~~~~~~nel~~~e~L~~~v~~l~~~f 96 (143)
..-.++-|++++|.+.+. ..-++++.+.++.-+|-
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 567789999999999854 34556777778777775
No 16
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=94.79 E-value=0.62 Score=32.72 Aligned_cols=93 Identities=12% Similarity=0.105 Sum_probs=57.1
Q ss_pred CceEEEEEEeCCCCEEEEecCcCCCHHHH----HHH---HHHHHHHHhcc-c--C-CCcceeEeCCEE-EEEEEeCcEEE
Q 032296 1 MGIRFILMVNKQGQTRLAQYYEWLTLEER----RAL---EGEIVRKCLAR-T--E-QQCSFVEHRNYK-IVYRRYASLFF 68 (143)
Q Consensus 1 mmI~~~~iln~~G~~il~k~Y~~~~~~~~----~~~---~~~~~~~~~~~-~--~-~~~~i~~~~~~~-~vy~~~~~l~f 68 (143)
|.+.+++|+|++|-.++.|-+.....+-- --+ ...++....+. + + ..--++..++.. .+|+...++-|
T Consensus 1 mave~~~iINksGglifqref~~~et~lnsneyLiLastlhgV~aI~tq~~p~~gssg~~~l~~~~f~m~I~qT~TG~kF 80 (134)
T COG5122 1 MAVEQFFIINKSGGLIFQREFGEGETELNSNEYLILASTLHGVSAILTQTIPLPGSSGRLVLYFRNFVMTIFQTTTGTKF 80 (134)
T ss_pred CceeEEEEEecCCcEEEEEeccCCccccCcccEEEEeechhhhhhhhhhcccCCCCCceEEEEeccEEEEEEEecCCcEE
Confidence 88999999999999999999964211100 000 11111111111 1 1 122345566655 57888899999
Q ss_pred EEEE-cCCcCHHHHHHHHHHHHHHHHhhh
Q 032296 69 LVGV-DNDENELAILEFIHLLVETMDRHF 96 (143)
Q Consensus 69 ~~~~-~~~~nel~~~e~L~~~v~~l~~~f 96 (143)
++++ +...|.++- ++.++....+|-
T Consensus 81 V~~~~k~t~na~~q---l~kiY~lYsdYV 106 (134)
T COG5122 81 VFVAEKRTVNALFQ---LQKIYSLYSDYV 106 (134)
T ss_pred EEEecCCchhHHHH---HHHHHHHHHHHh
Confidence 9999 556665544 667777777775
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=91.27 E-value=2.5 Score=27.15 Aligned_cols=48 Identities=17% Similarity=0.259 Sum_probs=41.7
Q ss_pred eeEeCCEEEEEEEeCcEEEEEEEcCCcCHHHHHHHHHHHHHHHHhhhc
Q 032296 50 FVEHRNYKIVYRRYASLFFLVGVDNDENELAILEFIHLLVETMDRHFG 97 (143)
Q Consensus 50 i~~~~~~~~vy~~~~~l~f~~~~~~~~nel~~~e~L~~~v~~l~~~f~ 97 (143)
.++.+++.+=|...+++.++|+++.+.+.-..+.||+.+.+-+..-++
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 466788888777789999999999999999999999999998888776
No 18
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=91.25 E-value=5.2 Score=30.25 Aligned_cols=46 Identities=9% Similarity=0.173 Sum_probs=35.9
Q ss_pred ceeEeCCEE-EEEEEeCcEEEEEEEcCCcCHHHHHHHHHHHHHHHHhhh
Q 032296 49 SFVEHRNYK-IVYRRYASLFFLVGVDNDENELAILEFIHLLVETMDRHF 96 (143)
Q Consensus 49 ~i~~~~~~~-~vy~~~~~l~f~~~~~~~~nel~~~e~L~~~v~~l~~~f 96 (143)
.+++.+..+ .+|....++-|+++++.-. -.+-.+|..+++...+|-
T Consensus 124 e~LetdtF~l~~~QTlTG~KFVvis~~~~--~~aD~lLrKiYelYsDyv 170 (199)
T KOG3369|consen 124 EVLETDTFTLHIFQTLTGTKFVVIAEPGT--QGADSLLRKIYELYSDYV 170 (199)
T ss_pred EEEEeccEEEEEEEccCCcEEEEEecCCc--hhHHHHHHHHHHHHHHHh
Confidence 455666655 4788888999999998776 466778999999988885
No 19
>KOG0997 consensus Uncharacterized conserved protein Sand [Function unknown]
Probab=90.32 E-value=4.8 Score=34.89 Aligned_cols=78 Identities=10% Similarity=0.140 Sum_probs=47.7
Q ss_pred EEEEEeCCCCEEEEecCcCCCHHHHHHHHHHHHHHHhcccCCCcceeEeCCEEEEEEEeCcEEEEEEEcCCcCHHHHHH
Q 032296 5 FILMVNKQGQTRLAQYYEWLTLEERRALEGEIVRKCLARTEQQCSFVEHRNYKIVYRRYASLFFLVGVDNDENELAILE 83 (143)
Q Consensus 5 ~~~iln~~G~~il~k~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~f~~~~~~~~nel~~~e 83 (143)
-+||++..|+++++++=.......-......+..-....+..-+. +...|+++++-+.+-++++|++..+..+--+..
T Consensus 119 hifilseaGKPiyS~~gs~e~l~stmGv~~alISf~q~~~~~i~s-i~a~g~k~vfl~kspl~LvA~s~t~~Sa~qL~~ 196 (523)
T KOG0997|consen 119 HIFILSEAGKPIYSRHGSDEALSSTMGVMQALISFFQVSGLAITS-IHAFGNKLVFLQKSPLLLVAVSRTSQSAAQLLQ 196 (523)
T ss_pred eEEEEecCCCceeeecCcHHHHHHHHHHHHHHHHHHhhCCceEEE-EEecCceEEEEecCcEEEEEEcccccCHHHHHH
Confidence 589999999999999965311100111111111111111112222 346899999999999999999998887665544
No 20
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=89.07 E-value=9.1 Score=29.73 Aligned_cols=94 Identities=16% Similarity=0.252 Sum_probs=64.1
Q ss_pred EEEEEEeCCCCEEEEecC---cC-CCHHHHHHHHHHHHHHHhcccCCCcceeEeCCEEEEEEEeCcEEEEEEEcCCcCHH
Q 032296 4 RFILMVNKQGQTRLAQYY---EW-LTLEERRALEGEIVRKCLARTEQQCSFVEHRNYKIVYRRYASLFFLVGVDNDENEL 79 (143)
Q Consensus 4 ~~~~iln~~G~~il~k~Y---~~-~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~f~~~~~~~~nel 79 (143)
...+.==.+|-++.+-.= ++ .+..+.++=.+.++++....++..|. ++.+.+.|=|...+++.+.+.++.+.+--
T Consensus 4 ~T~I~RV~DGLPLa~s~d~~e~~~~s~~e~r~q~K~L~kkLs~~s~~r~S-ietg~f~fHfli~~~Vcylvicd~~yP~k 82 (216)
T KOG0862|consen 4 LTLIARVRDGLPLAASTDDNEQSGDSLLEYRQQAKSLFKKLSQQSPTRCS-IETGPFVFHFLIESGVCYLVICDKSYPRK 82 (216)
T ss_pred eEEEEEecCCcccccccCcccCCCchHHHHHHHHHHHHHhccCCCCcccc-cccCCeEEEEEecCCEEEEEEecCCCcHH
Confidence 344444456666544322 12 23123333356667766443334444 45577888899999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhhcc
Q 032296 80 AILEFIHLLVETMDRHFGN 98 (143)
Q Consensus 80 ~~~e~L~~~v~~l~~~f~~ 98 (143)
+++.+|+.+.+-+.+-+|.
T Consensus 83 LAF~YLedL~~EF~~~~~~ 101 (216)
T KOG0862|consen 83 LAFSYLEDLAQEFDKSYGK 101 (216)
T ss_pred HHHHHHHHHHHHHHHhccc
Confidence 9999999999999998874
No 21
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=84.59 E-value=16 Score=28.12 Aligned_cols=87 Identities=16% Similarity=0.293 Sum_probs=57.2
Q ss_pred EEEeCCCCEEEEecCcCC-CHHHHHHHHHHHHHHHhcccCCCcceeEeCCEEEEEEEeCcEEEEEEEcCCcCHHHHHHHH
Q 032296 7 LMVNKQGQTRLAQYYEWL-TLEERRALEGEIVRKCLARTEQQCSFVEHRNYKIVYRRYASLFFLVGVDNDENELAILEFI 85 (143)
Q Consensus 7 ~iln~~G~~il~k~Y~~~-~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~f~~~~~~~~nel~~~e~L 85 (143)
+=+=.+|-++|++|=... +. ..+.+++-+++-.. ++.---..+|++.+=|.+-+++.++|+++.+..--.-+.||
T Consensus 5 Ys~VARGTvvLaeft~~~gNf---~sva~qiL~klp~~-~n~k~tYs~d~y~Fh~l~~dg~tylcvadds~gR~ipfaFL 80 (217)
T KOG0859|consen 5 YSFVARGTVILAEFTEFSGNF---SSIAAQILQKLPSS-SNSKFTYSCDGYTFHYLVEDGLTYLCVADDSAGRQIPFAFL 80 (217)
T ss_pred EEEEecceEEEEeeeeccCCH---HHHHHHHHHhCCCC-CCCceEEecCCeEEEEEEeCCeEEEEEEeccccccccHHHH
Confidence 334478999999986531 11 12222222333111 11122346799999999999999999999998888888888
Q ss_pred HHHHHHHHhhhc
Q 032296 86 HLLVETMDRHFG 97 (143)
Q Consensus 86 ~~~v~~l~~~f~ 97 (143)
.++-+-+.+=+|
T Consensus 81 e~Ik~~F~k~YG 92 (217)
T KOG0859|consen 81 ERIKEDFKKRYG 92 (217)
T ss_pred HHHHHHHHHHhc
Confidence 887776655554
No 22
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=81.44 E-value=18 Score=26.14 Aligned_cols=88 Identities=15% Similarity=0.287 Sum_probs=52.6
Q ss_pred CceEEEEEEeCCCCEEEEecCcC-----CCHHH-HHHHHHHHHHH---Hhccc--CCCcceeEe--CCEEEEE-EEeCcE
Q 032296 1 MGIRFILMVNKQGQTRLAQYYEW-----LTLEE-RRALEGEIVRK---CLART--EQQCSFVEH--RNYKIVY-RRYASL 66 (143)
Q Consensus 1 mmI~~~~iln~~G~~il~k~Y~~-----~~~~~-~~~~~~~~~~~---~~~~~--~~~~~i~~~--~~~~~vy-~~~~~l 66 (143)
|.|.++.|+|+.|.-++.+-|.. .++++ .+-.-.=+|.. +.+-+ +....+..+ ..++.-| -.-.+|
T Consensus 1 Mtiy~~yIFdR~g~Cl~y~EW~r~~~s~~~~eee~KL~yGmlFSlkS~v~Kls~~d~k~~f~sy~Ts~YklhfyeTptgl 80 (140)
T KOG3368|consen 1 MTIYNFYIFDRNGVCLFYREWNRTKQSGIPNEEEAKLMYGMLFSLKSFVSKLSPGDVKDGFLSYKTSKYKLHFYETPTGL 80 (140)
T ss_pred CeEEEEEEEcCCccEEEehhcccccccCCchhHHHHHHHHHHhhHHHHHHhcCCCCcccCeeEEeeceeEEEEEEcCCCc
Confidence 89999999999999998887752 23322 22222222321 22211 112223332 4455433 344589
Q ss_pred EEEEEEcCCcCHHHHHHHHHHHHH
Q 032296 67 FFLVGVDNDENELAILEFIHLLVE 90 (143)
Q Consensus 67 ~f~~~~~~~~nel~~~e~L~~~v~ 90 (143)
.|+..+|.+... +=++||.++.
T Consensus 81 k~vl~Tdpk~~~--ir~vLq~IYs 102 (140)
T KOG3368|consen 81 KFVLNTDPKAGS--IRDVLQYIYS 102 (140)
T ss_pred EEEEecCCCccc--HHHHHHHHHH
Confidence 999999988765 4577888777
No 23
>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=79.68 E-value=21 Score=25.97 Aligned_cols=73 Identities=11% Similarity=0.239 Sum_probs=33.4
Q ss_pred ceEEEEEEeCCCCEEEEecCcC--CCHHHHHHHHHHHHH-HHhcc-cCCCcceeEe-------CCEEEEEE--EeCcEEE
Q 032296 2 GIRFILMVNKQGQTRLAQYYEW--LTLEERRALEGEIVR-KCLAR-TEQQCSFVEH-------RNYKIVYR--RYASLFF 68 (143)
Q Consensus 2 mI~~~~iln~~G~~il~k~Y~~--~~~~~~~~~~~~~~~-~~~~~-~~~~~~i~~~-------~~~~~vy~--~~~~l~f 68 (143)
|+..+.|+..+|++++.-.=-+ .++....+|...+.. .+.+. .+....++.+ ++.+..|. +...|||
T Consensus 1 MfdQlaIFTpqGqvLyqyN~~gKKFsE~QiN~FIs~lItsP~~~~e~~~~~k~~~i~s~~~~~~~f~~mfh~sKQPeLy~ 80 (148)
T PF09201_consen 1 MFDQLAIFTPQGQVLYQYNCLGKKFSETQINAFISHLITSPVTKKEDSSKSKFLTISSEKKNSRSFSAMFHISKQPELYY 80 (148)
T ss_dssp ---EEEEE-TT-BEEEEEETTS----HHHHHHHHHHHHHS---GGGTT--EEEEE-----------EEEEEEETTTTEEE
T ss_pred CcceeEEeccCceEEEEecccchHHHHHHHHHHHHHHhcCCCcccCCCcceeeEEecccccCCCChheeeeecCCCcEEE
Confidence 8899999999999987532222 233333444443322 11111 1122334433 46666654 5778999
Q ss_pred EEEEcC
Q 032296 69 LVGVDN 74 (143)
Q Consensus 69 ~~~~~~ 74 (143)
+++-.+
T Consensus 81 VvTyae 86 (148)
T PF09201_consen 81 VVTYAE 86 (148)
T ss_dssp EEEESS
T ss_pred EEEecc
Confidence 998876
No 24
>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=68.61 E-value=56 Score=25.70 Aligned_cols=49 Identities=12% Similarity=0.123 Sum_probs=34.6
Q ss_pred eeEeCCEEEEEEEeCc--EEEEEEEcCCcCHHHHHHHHHHHHHHHHhhhcc
Q 032296 50 FVEHRNYKIVYRRYAS--LFFLVGVDNDENELAILEFIHLLVETMDRHFGN 98 (143)
Q Consensus 50 i~~~~~~~~vy~~~~~--l~f~~~~~~~~nel~~~e~L~~~v~~l~~~f~~ 98 (143)
-+.+++|.+=|+-.++ |.|+|+-..=-.-..+-++|..+...+.+.|+.
T Consensus 21 ~~~~d~y~lkw~~~Ne~~LvfVvvYq~il~l~yvd~LL~~v~~~F~~~y~~ 71 (279)
T PF04086_consen 21 SFTYDNYTLKWTLDNELGLVFVVVYQKILQLTYVDKLLDDVKKEFVKLYKN 71 (279)
T ss_dssp -------EEEEEEETTTTEEEEEEES-GGGHHHHHHHHHHHHHHHHHHTHH
T ss_pred ceeEcCEEEEEEEeccCCEEEeeeecccccchHHHHHHHHHHHHHHHHHhH
Confidence 3788999999998884 889999998888888888888888888887764
No 25
>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=63.34 E-value=18 Score=26.74 Aligned_cols=51 Identities=16% Similarity=0.103 Sum_probs=38.7
Q ss_pred HHHHHHhhhccccHHHHHhhHHHHHHHHHHHHhCcEEeec------CHHHHHHHHhh
Q 032296 88 LVETMDRHFGNVCELDIMFHLEKAHFMLEEMVMNGCIVET------SKSNILSPIQL 138 (143)
Q Consensus 88 ~v~~l~~~f~~v~e~~i~~nf~~vy~iLDEiid~G~~~eT------~~~~i~~~i~~ 138 (143)
+-+.|+++++++++++..+...-.-+.+||-..+|.-.+- +|+.+++.+..
T Consensus 6 fL~~L~~~L~~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG~P~~iA~~i~~ 62 (181)
T PF08006_consen 6 FLNELEKYLKKLPEEEREEILEYYEEYFDDAGEEGKSEEEIIAELGSPKEIAREILA 62 (181)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcCCHHHHHHHHHH
Confidence 3455788888899999999888888888888887764443 77777776653
No 26
>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=56.15 E-value=48 Score=20.79 Aligned_cols=62 Identities=13% Similarity=0.199 Sum_probs=34.2
Q ss_pred eEEEEEEeCCCCEEEEecCcCCCHHHHHHHH---HHHHHHHhc----ccCC--CcceeEeCCEEEEEEEeCcEE
Q 032296 3 IRFILMVNKQGQTRLAQYYEWLTLEERRALE---GEIVRKCLA----RTEQ--QCSFVEHRNYKIVYRRYASLF 67 (143)
Q Consensus 3 I~~~~iln~~G~~il~k~Y~~~~~~~~~~~~---~~~~~~~~~----~~~~--~~~i~~~~~~~~vy~~~~~l~ 67 (143)
+.+.+++|++|.++-+ +. .+....+.+. ..++....+ -+.. ..-.++.++..++..+.++=+
T Consensus 15 v~~~~l~~~dG~~i~~--~~-~~~~~~~~~aa~~a~~~~~~~~~~~~l~~~~~~~v~i~~~~~~i~i~~~~~~~ 85 (91)
T PF03259_consen 15 VRGAVLVDKDGLVIAS--SG-IDDDDAEKLAAMAASLLAAAEKLAKELGEGELEQVRIETEKGEIIITPVGDFY 85 (91)
T ss_dssp EEEEEEEETTSEEEEE--TS-SSHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEEEEEESSEEEEEEECSTCE
T ss_pred eeEEEEEcCCCCEEEE--ec-CCcccHHHHHHHHHHHHHHHHHHHHHhCCCCcEEEEEEECCCEEEEEEcCCCE
Confidence 6789999999999988 22 2222223322 333332211 1111 223456677777777777733
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=55.57 E-value=47 Score=23.26 Aligned_cols=21 Identities=14% Similarity=0.570 Sum_probs=17.8
Q ss_pred eEEEEEEeCCCCEEE--EecCcC
Q 032296 3 IRFILMVNKQGQTRL--AQYYEW 23 (143)
Q Consensus 3 I~~~~iln~~G~~il--~k~Y~~ 23 (143)
+.+++++|.+|+++. ++.+..
T Consensus 50 ~d~~~~~d~~g~~~~~~~~~~~~ 72 (161)
T PF05228_consen 50 LDLIFILDPDGRVLYSSSKGYDF 72 (161)
T ss_pred ccEEEEEcCCCCEEEEeccCccc
Confidence 578999999999998 777664
No 28
>COG3322 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]
Probab=55.32 E-value=11 Score=30.75 Aligned_cols=21 Identities=10% Similarity=0.248 Sum_probs=19.1
Q ss_pred eEEEEEEeCCCCEEEEecCcC
Q 032296 3 IRFILMVNKQGQTRLAQYYEW 23 (143)
Q Consensus 3 I~~~~iln~~G~~il~k~Y~~ 23 (143)
+.++|++|++|+++++|.+++
T Consensus 104 ~d~vf~vd~~G~~vy~~~~d~ 124 (295)
T COG3322 104 LDGVFVVDPSGKLVYSKLVDQ 124 (295)
T ss_pred ccEEEEECCCCCEEEEeeecc
Confidence 468999999999999999985
No 29
>PF08217 DUF1712: Fungal domain of unknown function (DUF1712); InterPro: IPR013176 The function of this fungal family of proteins is unknown.
Probab=54.40 E-value=1.3e+02 Score=26.92 Aligned_cols=73 Identities=16% Similarity=0.318 Sum_probs=49.8
Q ss_pred CCCcceeEeCCEEEEEE-EeCcEEEEEEEc-------CCcCHHHHHHHHHHHHHHHHhhhccccHHHHHhhHHHHHHHHH
Q 032296 45 EQQCSFVEHRNYKIVYR-RYASLFFLVGVD-------NDENELAILEFIHLLVETMDRHFGNVCELDIMFHLEKAHFMLE 116 (143)
Q Consensus 45 ~~~~~i~~~~~~~~vy~-~~~~l~f~~~~~-------~~~nel~~~e~L~~~v~~l~~~f~~v~e~~i~~nf~~vy~iLD 116 (143)
+..|..++.+..++++. .-++.|++++.+ .+.++-.+...|.+.+..+.-++|.++.. .++.......|+
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 44677777777776655 567999988877 22344468999999999999999975432 225555555555
Q ss_pred HHH
Q 032296 117 EMV 119 (143)
Q Consensus 117 Eii 119 (143)
+-.
T Consensus 133 ~F~ 135 (604)
T PF08217_consen 133 DFF 135 (604)
T ss_pred HHH
Confidence 544
No 30
>KOG0861 consensus SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=52.09 E-value=1e+02 Score=23.40 Aligned_cols=91 Identities=19% Similarity=0.205 Sum_probs=54.0
Q ss_pred CceEEEEEEeCCCCE--EEEecCc--C---CCHHHHHHHHHHHHHHHhcccC--CCcceeEeCCEE-EEEEEeCcEEEEE
Q 032296 1 MGIRFILMVNKQGQT--RLAQYYE--W---LTLEERRALEGEIVRKCLARTE--QQCSFVEHRNYK-IVYRRYASLFFLV 70 (143)
Q Consensus 1 mmI~~~~iln~~G~~--il~k~Y~--~---~~~~~~~~~~~~~~~~~~~~~~--~~~~i~~~~~~~-~vy~~~~~l~f~~ 70 (143)
|-|.++.++...+.. +++.-++ + .....-+.|.--+-+.+..|.+ .... +.++.+. .+|.|..+|--++
T Consensus 1 Mki~sl~V~~~~~~~~~ll~~a~dls~FsfFqRssV~Efm~F~sktvaeRt~~g~rqs-vk~~~Y~~h~yvrndgL~~V~ 79 (198)
T KOG0861|consen 1 MKIYSLSVLHKGTSDVKLLKTASDLSSFSFFQRSSVQEFMTFISKTVAERTGPGQRQS-VKHEEYLVHVYVRNDGLCGVL 79 (198)
T ss_pred CceEEEEEEeeCCcchhhhhhhcccccccceeeccHHHHHHHHHHHHHHhcCcccccc-cccceeEEEEEEecCCeeEEE
Confidence 678899999885443 3333333 1 1111122333222233444432 2333 3445555 4788888999999
Q ss_pred EEcCCcCHHHHHHHHHHHHHHH
Q 032296 71 GVDNDENELAILEFIHLLVETM 92 (143)
Q Consensus 71 ~~~~~~nel~~~e~L~~~v~~l 92 (143)
++|.+.+--..+.+|+.+-+-.
T Consensus 80 ~~D~eYP~rvA~tLL~kvld~~ 101 (198)
T KOG0861|consen 80 IADDEYPVRVAFTLLNKVLDEF 101 (198)
T ss_pred EecCcCchhHHHHHHHHHHHHH
Confidence 9999999999999888754443
No 31
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=51.22 E-value=1.8e+02 Score=25.83 Aligned_cols=111 Identities=12% Similarity=0.102 Sum_probs=64.1
Q ss_pred ceEEEEEEeCCCCEEEEecCcCCCHHHHHHHHHHHHHHH-hcccCCCcceeEeCCEEEEEEEeCc--EEEEEEEcCCcCH
Q 032296 2 GIRFILMVNKQGQTRLAQYYEWLTLEERRALEGEIVRKC-LARTEQQCSFVEHRNYKIVYRRYAS--LFFLVGVDNDENE 78 (143)
Q Consensus 2 mI~~~~iln~~G~~il~k~Y~~~~~~~~~~~~~~~~~~~-~~~~~~~~~i~~~~~~~~vy~~~~~--l~f~~~~~~~~ne 78 (143)
|+..+.|++..|-++....=-+...++ -...+++.+ ..+.+...+ +.++.+++=|...++ +.|+++-..--+=
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 888999999998765432222222222 234445543 232222222 667888888877665 5566666655555
Q ss_pred HHHHHHHHHHHHHHHhhhccccHHHHHhhHH-HHHHHHH
Q 032296 79 LAILEFIHLLVETMDRHFGNVCELDIMFHLE-KAHFMLE 116 (143)
Q Consensus 79 l~~~e~L~~~v~~l~~~f~~v~e~~i~~nf~-~vy~iLD 116 (143)
.++-.+|....+++..-|...+-..++-|+. ...++|+
T Consensus 77 ~yv~~ll~~v~~~f~e~~~~~~~~~l~~n~~~~~~e~lk 115 (587)
T KOG0781|consen 77 TYVDKLLNDVLNLFREKYDTQSALSLLNNTFDFQEELLK 115 (587)
T ss_pred hhHHHHHHHHHHHHHHHhccchHHHhhhhhHHHHHHHHH
Confidence 5566677777777776665555555555554 3344444
No 32
>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=50.13 E-value=29 Score=24.32 Aligned_cols=34 Identities=18% Similarity=0.258 Sum_probs=23.7
Q ss_pred HHHHHHhhhccccHHHHHhhHHHHHHHHHHHHhCcEE
Q 032296 88 LVETMDRHFGNVCELDIMFHLEKAHFMLEEMVMNGCI 124 (143)
Q Consensus 88 ~v~~l~~~f~~v~e~~i~~nf~~vy~iLDEiid~G~~ 124 (143)
+.+.|++=|+++. -.=|-..+|-.|+|++++|+.
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 3455666666654 555778999999999999998
No 33
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=46.23 E-value=21 Score=23.70 Aligned_cols=46 Identities=13% Similarity=0.078 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHh-hhc--cccHHHHHhh----HHHHHHHHHHHHhCcEEeecC
Q 032296 83 EFIHLLVETMDR-HFG--NVCELDIMFH----LEKAHFMLEEMVMNGCIVETS 128 (143)
Q Consensus 83 e~L~~~v~~l~~-~f~--~v~e~~i~~n----f~~vy~iLDEiid~G~~~eT~ 128 (143)
..-.++.+.++. .-. ++.-..|... -..|...+|++++.|++..|-
T Consensus 47 ~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTi 99 (102)
T PF08784_consen 47 PLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYSTI 99 (102)
T ss_dssp HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEESS
T ss_pred HHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEeccc
Confidence 334445555555 221 3555555544 479999999999999999884
No 34
>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=43.18 E-value=23 Score=17.29 Aligned_cols=18 Identities=28% Similarity=0.287 Sum_probs=14.8
Q ss_pred hhHHHHHHHHHHHHhCcE
Q 032296 106 FHLEKAHFMLEEMVMNGC 123 (143)
Q Consensus 106 ~nf~~vy~iLDEiid~G~ 123 (143)
.+++.+..+++||.+.|+
T Consensus 14 ~~~~~a~~~~~~M~~~g~ 31 (31)
T PF01535_consen 14 GQFEEALEVFDEMRERGI 31 (31)
T ss_pred chHHHHHHHHHHHhHCcC
Confidence 467888999999998874
No 35
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=37.47 E-value=29 Score=17.33 Aligned_cols=18 Identities=22% Similarity=0.226 Sum_probs=14.7
Q ss_pred hhHHHHHHHHHHHHhCcE
Q 032296 106 FHLEKAHFMLEEMVMNGC 123 (143)
Q Consensus 106 ~nf~~vy~iLDEiid~G~ 123 (143)
.+++.+..++++|...|+
T Consensus 15 g~~~~a~~~~~~M~~~gv 32 (34)
T PF13812_consen 15 GDPDAALQLFDEMKEQGV 32 (34)
T ss_pred CCHHHHHHHHHHHHHhCC
Confidence 356779999999998885
No 36
>KOG1373 consensus Transport protein Sec61, alpha subunit [Intracellular trafficking, secretion, and vesicular transport; Posttranslational modification, protein turnover, chaperones]
Probab=37.00 E-value=53 Score=28.02 Aligned_cols=50 Identities=18% Similarity=0.277 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHHhhhccccHHHHH----hhH-----HHHHHHHHHHHhCcEEeecCH
Q 032296 80 AILEFIHLLVETMDRHFGNVCELDIM----FHL-----EKAHFMLEEMVMNGCIVETSK 129 (143)
Q Consensus 80 ~~~e~L~~~v~~l~~~f~~v~e~~i~----~nf-----~~vy~iLDEiid~G~~~eT~~ 129 (143)
+++.+.+..+-++..++|..++...- =++ ..+..+|||+++-||=+.+-.
T Consensus 123 iii~vgqa~~yV~tG~yG~p~dLg~~~clLii~QL~~Agiiv~lLdEllqKGyGlgSGi 181 (476)
T KOG1373|consen 123 IIITVGQAVVYVMTGMYGSPSDLGVGICLLIILQLFFAGIIVILLDELLQKGYGLGSGI 181 (476)
T ss_pred HHHHHHHHHHHhhhcccCChhhcchhHHHHHHHHHHHhhHHHHHHHHHHHhccCcCcch
Confidence 45667788888889999965553322 222 356789999999998665533
No 37
>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=34.72 E-value=38 Score=20.08 Aligned_cols=15 Identities=27% Similarity=0.386 Sum_probs=10.8
Q ss_pred HHHHHHHHHhCcEEe
Q 032296 111 AHFMLEEMVMNGCIV 125 (143)
Q Consensus 111 vy~iLDEiid~G~~~ 125 (143)
.-+.|||++..|.+.
T Consensus 15 L~dtLDeli~~~~I~ 29 (49)
T PF02268_consen 15 LTDTLDELIQEGKIT 29 (49)
T ss_dssp HHHHHHHHHHTTSS-
T ss_pred HHHHHHHHHHcCCCC
Confidence 346788999888765
No 38
>PF14903 WG_beta_rep: WG containing repeat
Probab=32.35 E-value=54 Score=16.76 Aligned_cols=17 Identities=18% Similarity=0.478 Sum_probs=14.0
Q ss_pred EEeCCCCEEEEecCcCC
Q 032296 8 MVNKQGQTRLAQYYEWL 24 (143)
Q Consensus 8 iln~~G~~il~k~Y~~~ 24 (143)
++|.+|+.++.--|+..
T Consensus 3 ~id~~G~~vi~~~yd~i 19 (35)
T PF14903_consen 3 YIDKNGKIVIPPKYDEI 19 (35)
T ss_pred EEeCCCCEEEEccccCc
Confidence 67999999998888763
No 39
>KOG0903 consensus Phosphatidylinositol 4-kinase, involved in intracellular trafficking and secretion [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=31.81 E-value=2.7e+02 Score=25.98 Aligned_cols=93 Identities=14% Similarity=0.274 Sum_probs=55.7
Q ss_pred HHHHHHHHHH--HHH---hc-ccCCCcceeEeCCEEEEEEEeCcEEEEEEEcCCcC-HHHHHHHHHHHHHHHH-------
Q 032296 28 ERRALEGEIV--RKC---LA-RTEQQCSFVEHRNYKIVYRRYASLFFLVGVDNDEN-ELAILEFIHLLVETMD------- 93 (143)
Q Consensus 28 ~~~~~~~~~~--~~~---~~-~~~~~~~i~~~~~~~~vy~~~~~l~f~~~~~~~~n-el~~~e~L~~~v~~l~------- 93 (143)
.|+.|...+. ..+ +. ...++.+++....-.++|+-++ ++...+.++.+ |.+-+-+-.-+.|+|+
T Consensus 679 AQrNFvqSlagYSLvcYlLQvKDRHNGNILiD~EGHIIHIDFG--FmLsnsPgnvgFEsAPFKLT~EylEvmgG~~~d~F 756 (847)
T KOG0903|consen 679 AQRNFVQSLAGYSLVCYLLQVKDRHNGNILIDEEGHIIHIDFG--FMLSNSPGNVGFESAPFKLTTEYLEVMGGLDSDMF 756 (847)
T ss_pred HHHHHHHHHHHHHHHHHhhhcccccCCceEecCCCCEEEEeee--eEecCCCCCcccccCchhhHHHHHHHhcCCcHHHH
Confidence 4566665542 222 22 2346788887766778888776 22223333332 4444445555666666
Q ss_pred hhhccccH---HHHHhhHHHHHHHHHHHHhCcE
Q 032296 94 RHFGNVCE---LDIMFHLEKAHFMLEEMVMNGC 123 (143)
Q Consensus 94 ~~f~~v~e---~~i~~nf~~vy~iLDEiid~G~ 123 (143)
+||+.++. ..++.|.+++..+. ||+.+|-
T Consensus 757 dyfK~L~l~gf~a~RKhadrIv~lv-EiMq~~S 788 (847)
T KOG0903|consen 757 DYFKSLMLQGFMALRKHADRIVLLV-EIMQDGS 788 (847)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-HHhhccC
Confidence 56666666 45778999999998 6776643
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=31.32 E-value=35 Score=22.65 Aligned_cols=42 Identities=7% Similarity=0.156 Sum_probs=32.8
Q ss_pred HHHHHhhHHHHHHHHHHHHhCcEEeecCHHHHHHHHhhhhcc
Q 032296 101 ELDIMFHLEKAHFMLEEMVMNGCIVETSKSNILSPIQLMEKM 142 (143)
Q Consensus 101 e~~i~~nf~~vy~iLDEiid~G~~~eT~~~~i~~~i~~~~~~ 142 (143)
...++.+..-+-=+||.+.++|++.+-+-++|.+.=+.|||+
T Consensus 7 Re~LV~rI~~v~plLD~Ll~n~~it~E~y~~V~a~~T~qdkm 48 (85)
T cd08324 7 RELLVTHIRNTQCLVDNLLKNDYFSTEDAEIVCACPTQPDKV 48 (85)
T ss_pred HHHHHHHHHhhHHHHHHHhccCCccHHHHHHHHhCCCCHHHH
Confidence 355777788888899999999999888888887766666653
No 41
>PF15047 DUF4533: Protein of unknown function (DUF4533)
Probab=30.64 E-value=90 Score=24.40 Aligned_cols=38 Identities=24% Similarity=0.398 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHhhhc------cccH-HHHHhhHHHHHHHHHHH
Q 032296 81 ILEFIHLLVETMDRHFG------NVCE-LDIMFHLEKAHFMLEEM 118 (143)
Q Consensus 81 ~~e~L~~~v~~l~~~f~------~v~e-~~i~~nf~~vy~iLDEi 118 (143)
..+|-+.+.++++...| .+.| ..|++||+.+..++-||
T Consensus 19 ~~s~TN~L~elfN~~m~tqi~~i~mkEd~~IKd~~eqmi~~~kem 63 (225)
T PF15047_consen 19 LFSFTNTLTELFNSHMNTQILLIAMKEDSNIKDNFEQMIKIFKEM 63 (225)
T ss_pred HHHHHHHHHHHHHhccccceeeeeecccCcHHHHHHHHHHHHHHH
Confidence 35677888888888887 2444 45999999988888776
No 42
>COG1049 AcnB Aconitase B [Energy production and conversion]
Probab=29.96 E-value=76 Score=28.82 Aligned_cols=41 Identities=20% Similarity=0.200 Sum_probs=35.7
Q ss_pred cccHHHHHhhHHHHHHHHHHHHhCcEEeecCHHHHHHHHhhhhc
Q 032296 98 NVCELDIMFHLEKAHFMLEEMVMNGCIVETSKSNILSPIQLMEK 141 (143)
Q Consensus 98 ~v~e~~i~~nf~~vy~iLDEiid~G~~~eT~~~~i~~~i~~~~~ 141 (143)
.++++.+++-+..-.-++..||+.||= ++.++..|+..+++
T Consensus 601 kl~~e~iiEyL~sni~l~k~MIa~Gy~---d~rTL~rri~~me~ 641 (852)
T COG1049 601 KLNKEPIIEYLKSNIVLLKWMIAEGYG---DARTLERRIDKMEA 641 (852)
T ss_pred ecCchhHHHHHHHHHHHHHHHHHhccc---cHHHHHHHHHHHHH
Confidence 467888999888888999999999995 99999999987664
No 43
>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=29.79 E-value=44 Score=16.37 Aligned_cols=20 Identities=25% Similarity=0.228 Sum_probs=16.0
Q ss_pred hhHHHHHHHHHHHHhCcEEe
Q 032296 106 FHLEKAHFMLEEMVMNGCIV 125 (143)
Q Consensus 106 ~nf~~vy~iLDEiid~G~~~ 125 (143)
.+++.+..++++|...|...
T Consensus 14 ~~~~~a~~~~~~M~~~g~~p 33 (35)
T TIGR00756 14 GRVEEALELFKEMLERGIEP 33 (35)
T ss_pred CCHHHHHHHHHHHHHcCCCC
Confidence 35678899999999988754
No 44
>KOG4281 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.30 E-value=70 Score=25.04 Aligned_cols=36 Identities=22% Similarity=0.246 Sum_probs=28.8
Q ss_pred HHHHHHHHHHhhhccccHHHHHhhHHHHHHHHHHHH
Q 032296 84 FIHLLVETMDRHFGNVCELDIMFHLEKAHFMLEEMV 119 (143)
Q Consensus 84 ~L~~~v~~l~~~f~~v~e~~i~~nf~~vy~iLDEii 119 (143)
+.+++.++++.-|.+-.--..-+|+.++-.+|||+-
T Consensus 3 ~vq~l~ntck~~fs~~~pg~~~~nlqkLr~vLd~lk 38 (236)
T KOG4281|consen 3 FVQRLFNTCKEVFSTGGPGPFEENLQKLRSVLDELK 38 (236)
T ss_pred hhHHHHHHHHHHhcCCCCCccHHHHHHHHHHHhhCC
Confidence 578899999999965433356679999999999985
No 45
>PF13041 PPR_2: PPR repeat family
Probab=26.92 E-value=46 Score=18.66 Aligned_cols=23 Identities=22% Similarity=0.210 Sum_probs=19.1
Q ss_pred hhHHHHHHHHHHHHhCcEEeecC
Q 032296 106 FHLEKAHFMLEEMVMNGCIVETS 128 (143)
Q Consensus 106 ~nf~~vy~iLDEiid~G~~~eT~ 128 (143)
.+++.+..+++||...|....+.
T Consensus 17 ~~~~~a~~l~~~M~~~g~~P~~~ 39 (50)
T PF13041_consen 17 GKFEEALKLFKEMKKRGIKPDSY 39 (50)
T ss_pred cCHHHHHHHHHHHHHcCCCCCHH
Confidence 47889999999999999876543
No 46
>PRK05483 rplN 50S ribosomal protein L14; Validated
Probab=26.00 E-value=87 Score=22.07 Aligned_cols=26 Identities=19% Similarity=0.312 Sum_probs=22.1
Q ss_pred EEEEEEeCCCCEEEEecCcCCCHHHH
Q 032296 4 RFILMVNKQGQTRLAQYYEWLTLEER 29 (143)
Q Consensus 4 ~~~~iln~~G~~il~k~Y~~~~~~~~ 29 (143)
+|+.++|.+|+++=.|-+-+.+.+-+
T Consensus 82 NavVLin~~~~p~GTrI~Gpv~~elr 107 (122)
T PRK05483 82 NAAVLLNNDGEPRGTRIFGPVARELR 107 (122)
T ss_pred CEEEEECCCCCEeEeEEeccchHHHh
Confidence 47899999999999999999876543
No 47
>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=25.46 E-value=1.4e+02 Score=19.49 Aligned_cols=17 Identities=18% Similarity=0.047 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHhCcEEe
Q 032296 109 EKAHFMLEEMVMNGCIV 125 (143)
Q Consensus 109 ~~vy~iLDEiid~G~~~ 125 (143)
.....+++.+.|.|++.
T Consensus 25 ~~~~~il~~L~d~GyI~ 41 (88)
T PF09639_consen 25 SYWSDILRMLQDEGYIK 41 (88)
T ss_dssp HHHHHHHHHHHHHTSEE
T ss_pred HHHHHHHHHHHHCCCcc
Confidence 77788999999999994
No 48
>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=25.14 E-value=42 Score=21.74 Aligned_cols=40 Identities=13% Similarity=0.136 Sum_probs=28.5
Q ss_pred HHHHhhHHHHHHHHHHHHhCcEEeecCHHHHHHHHhhhhc
Q 032296 102 LDIMFHLEKAHFMLEEMVMNGCIVETSKSNILSPIQLMEK 141 (143)
Q Consensus 102 ~~i~~nf~~vy~iLDEiid~G~~~eT~~~~i~~~i~~~~~ 141 (143)
..++.+...|-.++|-+...|++-+.+-+.|...=+.+++
T Consensus 8 ~~Li~~v~~v~~ilD~L~~~~Vit~e~~~~I~a~~T~~~k 47 (82)
T cd08330 8 EALIARVTNVDPILDKLHGKKVITQEQYSEVRAEKTNQEK 47 (82)
T ss_pred HHHHHHHhhHHHHHHHHHHCCCCCHHHHHHHHcCCCcHHH
Confidence 4466677778888888888888877777777665444444
No 49
>PF13337 Lon_2: Putative ATP-dependent Lon protease
Probab=25.12 E-value=1.3e+02 Score=26.17 Aligned_cols=55 Identities=20% Similarity=0.196 Sum_probs=45.5
Q ss_pred CHHHHHHHHHHHHHHHHhhhccccHHHHHhhHHHHHHHHHHHHhCcEEeecCHHHHHHHHhhhhc
Q 032296 77 NELAILEFIHLLVETMDRHFGNVCELDIMFHLEKAHFMLEEMVMNGCIVETSKSNILSPIQLMEK 141 (143)
Q Consensus 77 nel~~~e~L~~~v~~l~~~f~~v~e~~i~~nf~~vy~iLDEiid~G~~~eT~~~~i~~~i~~~~~ 141 (143)
=|.+++|+| |..|+.+-+|..+.+..+.|-.+|. .-||---+.+.++.++....+
T Consensus 23 vP~yV~E~L------L~~yc~~~d~~~i~~g~e~v~~~l~----~~yv~~~e~e~iks~i~e~g~ 77 (457)
T PF13337_consen 23 VPSYVLEYL------LGRYCASDDEEEIEEGVEKVKEILA----KNYVRPDEAEKIKSRIREKGR 77 (457)
T ss_pred CChHHHHHH------HHhhcCCCCHHHHHHHHHHHHHHHH----HHcCChhHHHHHHHHHHhCCc
Confidence 378999998 8899999999999999999888886 456667788899999876543
No 50
>COG0450 AhpC Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=25.10 E-value=3e+02 Score=21.05 Aligned_cols=22 Identities=14% Similarity=0.206 Sum_probs=19.5
Q ss_pred ceEEEEEEeCCCCEEEEecCcC
Q 032296 2 GIRFILMVNKQGQTRLAQYYEW 23 (143)
Q Consensus 2 mI~~~~iln~~G~~il~k~Y~~ 23 (143)
...++||+|.+|.++..-+|..
T Consensus 123 a~R~~FIIDp~g~ir~~~v~~~ 144 (194)
T COG0450 123 ALRGTFIIDPDGVIRHILVNPL 144 (194)
T ss_pred ceeEEEEECCCCeEEEEEEecC
Confidence 3578999999999999999984
No 51
>TIGR01067 rplN_bact ribosomal protein L14, bacterial/organelle. This model distinguishes bacterial and most organellar examples of ribosomal protein L14 from all archaeal and eukaryotic forms.
Probab=24.32 E-value=96 Score=21.82 Aligned_cols=26 Identities=19% Similarity=0.254 Sum_probs=22.1
Q ss_pred EEEEEEeCCCCEEEEecCcCCCHHHH
Q 032296 4 RFILMVNKQGQTRLAQYYEWLTLEER 29 (143)
Q Consensus 4 ~~~~iln~~G~~il~k~Y~~~~~~~~ 29 (143)
+|+.++|.+|+++=.|-+-+.+.+-+
T Consensus 82 Na~VLin~~~~p~GTrI~Gpv~~elr 107 (122)
T TIGR01067 82 NACVLINKNKEPRGTRIFGPVARELR 107 (122)
T ss_pred ceEEEECCCCCEeeeEEEccchHHHh
Confidence 47899999999999999999876543
No 52
>PF09561 RE_HpaII: HpaII restriction endonuclease; InterPro: IPR019062 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This family includes HpaII, which recognises the double-stranded sequence CCGG and cleaves after C-1.
Probab=24.11 E-value=3.1e+02 Score=22.99 Aligned_cols=56 Identities=16% Similarity=0.347 Sum_probs=36.3
Q ss_pred eEEEEEEeCCCCEEEEecCcCCCHHHHHHHHHHHHHHHhcccCCCcceeEeCCEEEEEEEeCcEEE
Q 032296 3 IRFILMVNKQGQTRLAQYYEWLTLEERRALEGEIVRKCLARTEQQCSFVEHRNYKIVYRRYASLFF 68 (143)
Q Consensus 3 I~~~~iln~~G~~il~k~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~vy~~~~~l~f 68 (143)
.-+.+|.+.+|++++...|. |..|++=+|..+.--+++ ..-.++-.+|+.-+..||
T Consensus 292 ~gGyivV~~dGevlcYHiy~------rn~FedYL~~NTkle~~S----ssRh~fG~iy~enG~~yf 347 (355)
T PF09561_consen 292 TGGYIVVKEDGEVLCYHIYN------RNEFEDYLYNNTKLETPS----SSRHKFGFIYRENGEYYF 347 (355)
T ss_pred cceEEEEeCCCCEEEEEehh------HHHHHHHHHhcccccCCC----CCcccceEEEEECCEEEE
Confidence 35789999999999987764 357887777765421111 112345568887666655
No 53
>PF00741 Gas_vesicle: Gas vesicle protein; InterPro: IPR000638 Gas vesicles are small, hollow, gas filled protein structures found in several cyanobacterial and archaebacterial microorganisms []. They allow the positioning of the bacteria at the favourable depth for growth. Gas vesicles are hollow cylindrical tubes, closed by a hollow, conical cap at each end. Both the conical end caps and central cylinder are made up of 4-5 nm wide ribs that run at right angles to the long axis of the structure. Gas vesicles seem to be constituted of two different protein components, GVPa and GVPc. GVPa, a small protein of about 70 amino acid residues, is the main constituent of gas vesicles and form the essential core of the structure. The sequence of GVPa is extremely well conserved. GvpJ and gvpM, two proteins encoded in the cluster of genes required for gas vesicle synthesis in the archaebacteria Halobacterium salinarium and Halobacterium mediterranei (Haloferax mediterranei), have been found [] to be evolutionary related to GVPa. The exact function of these two proteins is not known, although they could be important for determining the shape determination gas vesicles. The N-terminal domain of Aphanizomenon flos-aquae protein gvpA/J is also related to GVPa.; GO: 0005198 structural molecule activity, 0012506 vesicle membrane
Probab=23.23 E-value=71 Score=18.04 Aligned_cols=18 Identities=11% Similarity=0.357 Sum_probs=14.8
Q ss_pred HHHHHHHHHhCcEEeecC
Q 032296 111 AHFMLEEMVMNGCIVETS 128 (143)
Q Consensus 111 vy~iLDEiid~G~~~eT~ 128 (143)
..+++|-+.|.|.+...+
T Consensus 2 L~d~LdriLdkGvVi~gd 19 (39)
T PF00741_consen 2 LVDLLDRILDKGVVIDGD 19 (39)
T ss_pred HHHHHHHHcCCceEEEEE
Confidence 467899999999998765
No 54
>PRK15360 pathogenicity island 2 effector protein SseE; Provisional
Probab=22.50 E-value=3.1e+02 Score=19.84 Aligned_cols=50 Identities=10% Similarity=0.085 Sum_probs=30.6
Q ss_pred eeEeCCEEEEEEE-eCcEEEEEEEcCC---cCHHHHHHHHHHHHHHHHhhhccccHHH
Q 032296 50 FVEHRNYKIVYRR-YASLFFLVGVDND---ENELAILEFIHLLVETMDRHFGNVCELD 103 (143)
Q Consensus 50 i~~~~~~~~vy~~-~~~l~f~~~~~~~---~nel~~~e~L~~~v~~l~~~f~~v~e~~ 103 (143)
-+.++++.++||- -+.+++|..-..+ ..|..++.++ +.|...|+++.+..
T Consensus 30 ~~~~~g~~lvyRvE~~eliIc~lrR~~~~~~~p~~~~~L~----~~L~~l~~~~p~l~ 83 (137)
T PRK15360 30 QFILSPYLVIYRIEAKEMIICEFRRLTPGQPRPQQLFHLL----GLLRGIFVHHPQLT 83 (137)
T ss_pred EEEEcCEEEEEEecCCEEEEEEEEeccCCCCCHHHHHHHH----HHHHHHHccChHHH
Confidence 3568999999995 4457777666544 3355554444 44666666554433
No 55
>CHL00057 rpl14 ribosomal protein L14
Probab=21.46 E-value=1.2e+02 Score=21.44 Aligned_cols=25 Identities=8% Similarity=0.230 Sum_probs=21.5
Q ss_pred EEEEEEeCCCCEEEEecCcCCCHHH
Q 032296 4 RFILMVNKQGQTRLAQYYEWLTLEE 28 (143)
Q Consensus 4 ~~~~iln~~G~~il~k~Y~~~~~~~ 28 (143)
+|+.++|.+|+++=.|-+-+.+.+-
T Consensus 82 Na~VLin~~~~p~GTrI~Gpv~~el 106 (122)
T CHL00057 82 NAAVVIDQEGNPKGTRVFGPIAREL 106 (122)
T ss_pred ceEEEECCCCCEeEeEEEccchHHH
Confidence 4789999999999999999877553
No 56
>cd04685 Nudix_Hydrolase_26 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily requires a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=20.58 E-value=1.1e+02 Score=21.18 Aligned_cols=19 Identities=5% Similarity=0.139 Sum_probs=15.7
Q ss_pred EEEEEEeCCCCEEEEecCc
Q 032296 4 RFILMVNKQGQTRLAQYYE 22 (143)
Q Consensus 4 ~~~~iln~~G~~il~k~Y~ 22 (143)
..++++|.+|++++.|..+
T Consensus 3 ~~~~i~~~~g~vLl~r~~~ 21 (133)
T cd04685 3 ARVVLLDPDDRVLLLRGDD 21 (133)
T ss_pred EEEEEEcCCCeEEEEEEeC
Confidence 3678999999999988753
No 57
>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=20.49 E-value=1.1e+02 Score=21.27 Aligned_cols=19 Identities=11% Similarity=0.272 Sum_probs=15.6
Q ss_pred EEEEEEeCCCCEEEEecCc
Q 032296 4 RFILMVNKQGQTRLAQYYE 22 (143)
Q Consensus 4 ~~~~iln~~G~~il~k~Y~ 22 (143)
-+++|+|.+|++++.|.++
T Consensus 6 v~~ii~~~~~~vLL~~r~~ 24 (147)
T cd03671 6 VGVVLFNEDGKVFVGRRID 24 (147)
T ss_pred EEEEEEeCCCEEEEEEEcC
Confidence 3678889999999988766
Done!