Query 033113
Match_columns 127
No_of_seqs 120 out of 571
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 09:57:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033113.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033113hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5030 APS2 Clathrin adaptor 100.0 3E-54 6.5E-59 313.7 11.7 125 1-125 1-128 (152)
2 KOG0934 Clathrin adaptor compl 100.0 1E-51 2.2E-56 299.6 7.0 125 1-125 1-128 (145)
3 KOG0936 Clathrin adaptor compl 100.0 3.9E-50 8.4E-55 296.7 12.3 124 1-124 1-133 (182)
4 KOG0935 Clathrin adaptor compl 100.0 1.6E-49 3.5E-54 283.6 9.2 124 1-124 1-128 (143)
5 PF01217 Clat_adaptor_s: Clath 100.0 1.7E-38 3.7E-43 230.5 15.3 125 1-125 1-128 (141)
6 KOG3343 Vesicle coat complex C 99.9 8.8E-26 1.9E-30 167.9 12.0 121 2-125 9-136 (175)
7 KOG0938 Adaptor complexes medi 99.8 3.1E-19 6.8E-24 146.6 10.4 121 1-125 1-125 (446)
8 COG5541 RET3 Vesicle coat comp 99.7 2.2E-16 4.7E-21 117.7 10.0 121 2-125 8-143 (187)
9 KOG0937 Adaptor complexes medi 99.2 1.3E-10 2.9E-15 98.0 12.1 121 2-124 1-125 (424)
10 KOG2740 Clathrin-associated pr 98.9 9.2E-09 2E-13 85.6 8.4 120 1-125 1-128 (418)
11 KOG2635 Medium subunit of clat 97.9 0.00022 4.7E-09 61.2 11.0 114 3-118 4-120 (512)
12 PF15001 AP-5_subunit_s1: AP-5 95.5 0.14 3.1E-06 39.5 8.8 67 54-120 103-173 (189)
13 PF08923 MAPKK1_Int: Mitogen-a 93.6 1 2.3E-05 32.1 8.9 91 2-93 17-114 (119)
14 PF03164 Mon1: Trafficking pro 91.5 3.5 7.7E-05 35.0 10.9 76 4-82 13-90 (415)
15 PF04099 Sybindin: Sybindin-li 76.8 26 0.00056 25.4 11.9 92 2-94 1-114 (142)
16 COG3322 Predicted periplasmic 73.6 2.5 5.5E-05 34.7 2.2 23 2-24 104-126 (295)
17 PF13774 Longin: Regulated-SNA 62.7 38 0.00082 21.7 8.4 48 49-96 18-65 (83)
18 KOG0862 Synaptobrevin/VAMP-lik 56.9 97 0.0021 24.5 10.8 96 1-97 1-101 (216)
19 KOG3368 Transport protein part 50.8 99 0.0022 22.8 10.5 85 2-89 3-102 (140)
20 PRK13190 putative peroxiredoxi 46.1 35 0.00076 25.8 4.0 22 2-23 117-138 (202)
21 COG5122 TRS23 Transport protei 43.6 1.2E+02 0.0027 21.9 8.1 90 2-94 3-105 (134)
22 cd03016 PRX_1cys Peroxiredoxin 42.7 50 0.0011 24.9 4.3 21 2-22 117-137 (203)
23 KOG0859 Synaptobrevin/VAMP-lik 40.2 1.9E+02 0.004 22.9 9.9 76 9-88 8-84 (217)
24 PRK13599 putative peroxiredoxi 36.9 49 0.0011 25.5 3.5 21 2-22 119-139 (215)
25 PF09201 SRX: SRX; InterPro: 35.5 1.2E+02 0.0026 22.6 5.2 90 1-95 1-103 (148)
26 KOG0781 Signal recognition par 34.6 84 0.0018 28.2 4.9 67 1-71 1-70 (587)
27 PRK13191 putative peroxiredoxi 32.1 87 0.0019 24.0 4.2 21 2-22 124-144 (215)
28 PF05228 CHASE4: CHASE4 domain 30.6 1.9E+02 0.0041 20.1 6.4 21 2-22 50-72 (161)
29 PF13867 SAP30_Sin3_bdg: Sin3 29.8 66 0.0014 19.5 2.6 22 87-108 26-49 (53)
30 cd03015 PRX_Typ2cys Peroxiredo 29.2 1.1E+02 0.0023 22.1 4.1 35 3-37 121-155 (173)
31 KOG0854 Alkyl hydroperoxide re 29.0 52 0.0011 25.7 2.5 35 2-36 131-165 (224)
32 PRK13189 peroxiredoxin; Provis 27.6 1.1E+02 0.0024 23.6 4.1 20 2-21 126-145 (222)
33 PTZ00253 tryparedoxin peroxida 27.1 1.1E+02 0.0024 22.8 4.0 20 2-21 127-146 (199)
34 PRK15000 peroxidase; Provision 24.3 1.4E+02 0.003 22.6 4.1 20 2-21 125-144 (200)
35 PTZ00137 2-Cys peroxiredoxin; 24.1 1.2E+02 0.0026 24.3 3.9 21 2-22 188-208 (261)
36 PRK13728 conjugal transfer pro 23.5 1.6E+02 0.0034 22.5 4.2 35 4-38 139-173 (181)
37 COG0450 AhpC Peroxiredoxin [Po 21.9 86 0.0019 24.4 2.5 33 2-34 124-159 (194)
38 PF02791 DDT: DDT domain; Int 21.0 93 0.002 19.1 2.1 18 76-93 6-23 (61)
No 1
>COG5030 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]
Probab=100.00 E-value=3e-54 Score=313.74 Aligned_cols=125 Identities=51% Similarity=0.871 Sum_probs=123.2
Q ss_pred CeEEEEeecCCCCceeeecCCCCChHHHHHHHHHHhhhhcCCCCCccceEEeCCeEEEEEeeccEEEEEEecCCccHHHH
Q 033113 1 MIRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRLVVNRDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNELAY 80 (127)
Q Consensus 1 MI~~vli~n~~Gk~rl~K~Y~~~~~~~~~~~~~~v~~~v~~r~~~~~~~~~~~~~~ivYrrya~L~f~~~~d~~eNel~~ 80 (127)
||+|+|++|+|||+||+|||+|.+.++|+++++++++++++|++++|||+++.+.|+||||||+|||++++|++||||++
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 HHHHHHHHHHHHHHhhhhchhHHHHhHHHHH---HHHHhCCEeeeccc
Q 033113 81 LECIHLFVEILDHFFSNVCELDLVFNFHKVC---DRIFISSSVTVSFC 125 (127)
Q Consensus 81 le~I~~~ve~Ld~~f~nVcEldii~nf~k~~---DE~i~~G~v~e~~~ 125 (127)
||+||.|||+||+|||||||||+||||.|+| |||+.||+++||..
T Consensus 81 L~lIh~FVE~lDr~FgnVCELdlIFNF~kv~~ILdE~i~gG~i~Es~~ 128 (152)
T COG5030 81 LELIHNFVEILDRFFGNVCELDLIFNFQKVYAILDEMILGGEIIESSK 128 (152)
T ss_pred HHHHHHHHHHHHHHhccceeeEeEeeHHHHHHHHHHHHhCCeeeecCH
Confidence 9999999999999999999999999999999 99999999999864
No 2
>KOG0934 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1e-51 Score=299.61 Aligned_cols=125 Identities=48% Similarity=0.860 Sum_probs=122.7
Q ss_pred CeEEEEeecCCCCceeeecCCCCChHHHHHHHHHHhhhhcCCCCCccceEEeCCeEEEEEeeccEEEEEEecCCccHHHH
Q 033113 1 MIRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRLVVNRDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNELAY 80 (127)
Q Consensus 1 MI~~vli~n~~Gk~rl~K~Y~~~~~~~~~~~~~~v~~~v~~r~~~~~~~~~~~~~~ivYrrya~L~f~~~~d~~eNel~~ 80 (127)
||+|++++|+|||+||+|||.+.+.++|+++++++.+.+++|++++|+|+++++.|+||||||+|||+++++.+||||++
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 HHHHHHHHHHHHHHhhhhchhHHHHhHHHHH---HHHHhCCEeeeccc
Q 033113 81 LECIHLFVEILDHFFSNVCELDLVFNFHKVC---DRIFISSSVTVSFC 125 (127)
Q Consensus 81 le~I~~~ve~Ld~~f~nVcEldii~nf~k~~---DE~i~~G~v~e~~~ 125 (127)
||+||.|||+||+|||||||||+||||+|+| ||++.+|+++|+.-
T Consensus 81 LE~IH~~vE~lDkYFg~VCELDiiFNfekay~ILde~~~~g~~~e~~k 128 (145)
T KOG0934|consen 81 LEFIHNYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEIQETSK 128 (145)
T ss_pred HHHHHHHHHHHHHHhccceeeEEEEehHhHHHHHHHHhcCcchHhhhc
Confidence 9999999999999999999999999999999 99999999988753
No 3
>KOG0936 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=3.9e-50 Score=296.66 Aligned_cols=124 Identities=41% Similarity=0.740 Sum_probs=120.9
Q ss_pred CeEEEEeecCCCCceeeecCCCCChHHHHHHHHHHhhhhcCCCCCccceEEe----C--CeEEEEEeeccEEEEEEecCC
Q 033113 1 MIRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRLVVNRDPKFTNFVEF----R--THKVIYRRYAGLFFSLCVDIT 74 (127)
Q Consensus 1 MI~~vli~n~~Gk~rl~K~Y~~~~~~~~~~~~~~v~~~v~~r~~~~~~~~~~----~--~~~ivYrrya~L~f~~~~d~~ 74 (127)
||+|++|+|++|||||+|||+|.+.+.||++++++|..+++|++..|||++- + +.+++||+||+|||++|+|++
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 9999999999999999999999999999999999999999999999999985 3 799999999999999999999
Q ss_pred ccHHHHHHHHHHHHHHHHHHhhhhchhHHHHhHHHHH---HHHHhCCEeeecc
Q 033113 75 DNELAYLECIHLFVEILDHFFSNVCELDLVFNFHKVC---DRIFISSSVTVSF 124 (127)
Q Consensus 75 eNel~~le~I~~~ve~Ld~~f~nVcEldii~nf~k~~---DE~i~~G~v~e~~ 124 (127)
||||++||+||.|||+||++|+|||||||+||++|+| +|+++||+|+||-
T Consensus 81 EsEL~iLDLIQvfVEtLDkCF~nVcELDliF~~~k~h~iL~EiV~GGmVlETn 133 (182)
T KOG0936|consen 81 ESELGILDLIQVFVETLDKCFENVCELDLIFNWQKVHAILAEIVMGGMVLETN 133 (182)
T ss_pred cchhHHHHHHHHHHHHHHHHHHhhhhhhheeeHHHHHHHHHHHHhCCeEEecc
Confidence 9999999999999999999999999999999999999 9999999999984
No 4
>KOG0935 consensus Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.6e-49 Score=283.62 Aligned_cols=124 Identities=68% Similarity=1.122 Sum_probs=118.5
Q ss_pred CeEEEEeecCCCCceeeecCCCCChHHHHHHHHHHhhhhcCCCCCccceEEeCCeEEEEE-eeccEEEEEEecCCccHHH
Q 033113 1 MIRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRLVVNRDPKFTNFVEFRTHKVIYR-RYAGLFFSLCVDITDNELA 79 (127)
Q Consensus 1 MI~~vli~n~~Gk~rl~K~Y~~~~~~~~~~~~~~v~~~v~~r~~~~~~~~~~~~~~ivYr-rya~L~f~~~~d~~eNel~ 79 (127)
||+|+|++|++||+||+|||.|.+.+++++++.+|++++++|+++..|+++.++.|++|| |||+|||++|+|..+||++
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 999999999999999999999999999999999999999999999988888777776655 8999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhhchhHHHHhHHHHH---HHHHhCCEeeecc
Q 033113 80 YLECIHLFVEILDHFFSNVCELDLVFNFHKVC---DRIFISSSVTVSF 124 (127)
Q Consensus 80 ~le~I~~~ve~Ld~~f~nVcEldii~nf~k~~---DE~i~~G~v~e~~ 124 (127)
+||.||.|||+||.||+||||||++|||+|+| |||+.||+++||.
T Consensus 81 yLe~IHlFVEvLd~fF~NVCELDlvFNFyKVy~i~DEm~l~GEi~Ets 128 (143)
T KOG0935|consen 81 YLEHIHLFVEVLDEFFHNVCELDLVFNFYKVYTIVDEMFLAGEIRETS 128 (143)
T ss_pred HHHHHHHHHHHHHHHhccccceeeeeeeeeHHHHHHHHHHhhhhhhhh
Confidence 99999999999999999999999999999999 9999999999984
No 5
>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=1.7e-38 Score=230.46 Aligned_cols=125 Identities=34% Similarity=0.552 Sum_probs=119.0
Q ss_pred CeEEEEeecCCCCceeeecCCCCChHHHHHHHHHHhhhhcCCCCCccceEEeCCeEEEEEeeccEEEEEEecCCccHHHH
Q 033113 1 MIRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRLVVNRDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNELAY 80 (127)
Q Consensus 1 MI~~vli~n~~Gk~rl~K~Y~~~~~~~~~~~~~~v~~~v~~r~~~~~~~~~~~~~~ivYrrya~L~f~~~~d~~eNel~~ 80 (127)
||+|++|+|++|+++++|||.+.+.++++++.+++.+.+.+|+++.||++.++++++|||++++|||+++++.++||+++
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 99999999999999999999999999999999999999888988889999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhhhchhHHHHhHHHHH---HHHHhCCEeeeccc
Q 033113 81 LECIHLFVEILDHFFSNVCELDLVFNFHKVC---DRIFISSSVTVSFC 125 (127)
Q Consensus 81 le~I~~~ve~Ld~~f~nVcEldii~nf~k~~---DE~i~~G~v~e~~~ 125 (127)
+|+||.++++|+.|||+|||+++++||+++| |||+++|+|+||.+
T Consensus 81 ~e~l~~~v~~l~~~~~~v~e~~i~~N~~~v~~~LDEiid~G~i~etd~ 128 (141)
T PF01217_consen 81 LEFLHRLVEVLDDYFGNVSEKDILENFDLVYLILDEIIDGGIILETDP 128 (141)
T ss_dssp HHHHHHHHHHHHHHHSS-SHHHHHHTHHHHHHHHHHHEETTEES--TH
T ss_pred HHHHHHhhhhhhhhhccccHHHHHHCHHHHHHHHHHHHhCCEEEECCH
Confidence 9999999999999999999999999999999 99999999999975
No 6
>KOG3343 consensus Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.93 E-value=8.8e-26 Score=167.88 Aligned_cols=121 Identities=21% Similarity=0.303 Sum_probs=113.1
Q ss_pred eEEEEeecCCCCceeeecCCC--CC-hHHHHHHHHHHhhhhcCCCCCccceEEeCCeEEEEEeeccEEEEEEecCCccHH
Q 033113 2 IRFILLQNRQGKTRLAKYYVP--LE-DSEKHKVEYEVHRLVVNRDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNEL 78 (127)
Q Consensus 2 I~~vli~n~~Gk~rl~K~Y~~--~~-~~~~~~~~~~v~~~v~~r~~~~~~~~~~~~~~ivYrrya~L~f~~~~d~~eNel 78 (127)
+++++|+|++|++.++|||.+ ++ .++|+.+|+.+|+++++ ..+.++.++|.++|||.+-+|+|++++...||||
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 689999999999999999985 34 88999999999998874 3477999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHh-hhhchhHHHHhHHHHH---HHHHhCCEeeeccc
Q 033113 79 AYLECIHLFVEILDHFF-SNVCELDLVFNFHKVC---DRIFISSSVTVSFC 125 (127)
Q Consensus 79 ~~le~I~~~ve~Ld~~f-~nVcEldii~nf~k~~---DE~i~~G~v~e~~~ 125 (127)
.+.+.++++.++++..+ .||.+..++.|+|.++ |||+++|.|+||+|
T Consensus 86 ~L~svL~~l~dal~llLr~nveKr~llEN~D~i~L~~DEiiD~GvILEtdp 136 (175)
T KOG3343|consen 86 MLMSVLTCLFDALSLLLRKNVEKRELLENLDLIFLALDEIIDGGVILETDP 136 (175)
T ss_pred HHHHHHHHHHHHHHHHHHhChhHHHHHhhhccceeehhhhccCceEEecCH
Confidence 99999999999999999 5799999999999999 99999999999986
No 7
>KOG0938 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.80 E-value=3.1e-19 Score=146.58 Aligned_cols=121 Identities=15% Similarity=0.174 Sum_probs=116.2
Q ss_pred CeEEEEeecCCCCceeeecCCCCChHHHHHHHHHHhhh-hcCCCCCccceEEeCCeEEEEEeeccEEEEEEecCCccHHH
Q 033113 1 MIRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRL-VVNRDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNELA 79 (127)
Q Consensus 1 MI~~vli~n~~Gk~rl~K~Y~~~~~~~~~~~~~~v~~~-v~~r~~~~~~~~~~~~~~ivYrrya~L~f~~~~d~~eNel~ 79 (127)
||.+++++|.+|++.++|.|.+ +-++...++||. +++..+.+||++..++++++|-|..+||.++++.+|.|-.+
T Consensus 1 misglfi~n~rGevlink~fr~----dlkrs~~diFRv~vi~n~d~r~PV~~igsttf~~~r~~nl~lvaitksN~Nva~ 76 (446)
T KOG0938|consen 1 MISGLFIYNLRGEVLINKTFRD----DLKRSIVDIFRVQVINNLDVRSPVLTIGSTTFHHIRSSNLWLVAITKSNANVAA 76 (446)
T ss_pred CcceEEEEeccCcEEEehhhhh----hhhhhHHHHHHHhhhhccccCCCeeEecceeEEEEeeccEEEEEEecCCCchhh
Confidence 8999999999999999999998 899999999998 77776778999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhhchhHHHHhHHHHH---HHHHhCCEeeeccc
Q 033113 80 YLECIHLFVEILDHFFSNVCELDLVFNFHKVC---DRIFISSSVTVSFC 125 (127)
Q Consensus 80 ~le~I~~~ve~Ld~~f~nVcEldii~nf~k~~---DE~i~~G~v~e~~~ 125 (127)
++||+..++..+..|||...|..|..||..+| |||++.|++++|-+
T Consensus 77 v~eFl~kl~avm~aYfgk~~Eeaiknnf~lI~ElLDemld~G~pqnte~ 125 (446)
T KOG0938|consen 77 VFEFLYKLDAVMNAYFGKDREEAIKNNFVLIYELLDEMLDFGIPQNTEP 125 (446)
T ss_pred HHHHHHHHHHHHHHHhcccchhhhhhceEeHHHHHHHHHhcCCCccCCh
Confidence 99999999999999999999999999999999 99999999998864
No 8
>COG5541 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]
Probab=99.69 E-value=2.2e-16 Score=117.73 Aligned_cols=121 Identities=13% Similarity=0.202 Sum_probs=109.8
Q ss_pred eEEEEeecCCCCceeeecCCCC-----------ChHHHHHHHHHHhhhhcCCCCCccceEEeCCeEEEEEeeccEEEEEE
Q 033113 2 IRFILLQNRQGKTRLAKYYVPL-----------EDSEKHKVEYEVHRLVVNRDPKFTNFVEFRTHKVIYRRYAGLFFSLC 70 (127)
Q Consensus 2 I~~vli~n~~Gk~rl~K~Y~~~-----------~~~~~~~~~~~v~~~v~~r~~~~~~~~~~~~~~ivYrrya~L~f~~~ 70 (127)
++|+||+|+||++..+|||.|+ |-++++.+++.+++++.+ .+++++.+.+.-++|+|+-++.++.+
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 VEALLILDSQGERIYRKYYQPPHRSEGHQLVFNSVKKEKEFEKKLAEKTAK---DRESILMFYDRLVMCKRLDDVLLYIV 84 (187)
T ss_pred eeeeEEecCCccchhhhhcCCcccccccchhhcchhHHHHHHHHHHHHhhc---CccceeeEcceeeeeeeehhEEEEEe
Confidence 6899999999999999999875 677899999999997653 23679999999999999999999999
Q ss_pred ecCCccHHHHHHHHHHHHHHHHHHhhhh-chhHHHHhHHHHH---HHHHhCCEeeeccc
Q 033113 71 VDITDNELAYLECIHLFVEILDHFFSNV-CELDLVFNFHKVC---DRIFISSSVTVSFC 125 (127)
Q Consensus 71 ~d~~eNel~~le~I~~~ve~Ld~~f~nV-cEldii~nf~k~~---DE~i~~G~v~e~~~ 125 (127)
..-+|||..+.+....+..+|+..|..+ .+..+..|||.+- ||.+++|.|+||.+
T Consensus 85 ~~meeNE~~l~q~f~~ir~Al~li~k~~~dkr~v~enYDqivl~vdEtid~Gvilet~s 143 (187)
T COG5541 85 SPMEENEPFLGQVFDEIRAALILIVKTPTDKRNVWENYDQIVLLVDETIDEGVILETKS 143 (187)
T ss_pred cccccccHHHHHHHHHHHHHHHHHHcCCcchhhHHhhhceEEEeeehhcccceEeecCh
Confidence 9999999999999999999999999875 5666999999988 99999999999864
No 9
>KOG0937 consensus Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.23 E-value=1.3e-10 Score=97.96 Aligned_cols=121 Identities=12% Similarity=0.138 Sum_probs=102.6
Q ss_pred eEEEEeecCCCCceeeecCCC-CChHHHHHHHHHHhhhhcCCCCCccceEEeCCeEEEEEeeccEEEEEEecCCccHHHH
Q 033113 2 IRFILLQNRQGKTRLAKYYVP-LEDSEKHKVEYEVHRLVVNRDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNELAY 80 (127)
Q Consensus 2 I~~vli~n~~Gk~rl~K~Y~~-~~~~~~~~~~~~v~~~v~~r~~~~~~~~~~~~~~ivYrrya~L~f~~~~d~~eNel~~ 80 (127)
+++++++|.+|+++++|=|.. .+...--++....+.+. -.+...+++..++...+|-++.+||+++++..|.|...+
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 478999999999999998863 33334344444333332 123347899999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhhhchhHHHHhHHHHH---HHHHhCCEeeecc
Q 033113 81 LECIHLFVEILDHFFSNVCELDLVFNFHKVC---DRIFISSSVTVSF 124 (127)
Q Consensus 81 le~I~~~ve~Ld~~f~nVcEldii~nf~k~~---DE~i~~G~v~e~~ 124 (127)
+++++.+++++..||+.+.|+.+..||..+| ||+++.|.+|.|.
T Consensus 79 ~~~l~~~~~v~~~y~~~l~e~si~~n~vlvyElLde~mDFGypQ~t~ 125 (424)
T KOG0937|consen 79 LSFLYAVADVFGDYLSELEEESIRDNFVLVYELLDEVMDFGYPQTTD 125 (424)
T ss_pred HHHHHHHHHHHHHHhccCCccceecchHHHHHHHHHHhccCCcccch
Confidence 9999999999999999999999999999999 9999999998775
No 10
>KOG2740 consensus Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.87 E-value=9.2e-09 Score=85.60 Aligned_cols=120 Identities=19% Similarity=0.209 Sum_probs=87.1
Q ss_pred CeEEEEeecCCCCceeeecCCCCChHHHHHHHHHH-hhhhcC--CCCCccceEEeCCeEE--EEEeeccEEEEEEecCCc
Q 033113 1 MIRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEV-HRLVVN--RDPKFTNFVEFRTHKV--IYRRYAGLFFSLCVDITD 75 (127)
Q Consensus 1 MI~~vli~n~~Gk~rl~K~Y~~~~~~~~~~~~~~v-~~~v~~--r~~~~~~~~~~~~~~i--vYrrya~L~f~~~~d~~e 75 (127)
||+++++.|..|+..|.|-.+.. .+.+.+-+. +..-.+ +.+..-+++....+.+ +||. .++||++.-..-
T Consensus 1 mi~siflidtsg~l~lek~~~g~---t~~rsic~~f~e~~~~~~~~e~~ppvi~~p~hylfsv~~~--~i~~~~~st~e~ 75 (418)
T KOG2740|consen 1 MILSIFLIDTSGDLLLEKHLKGS---TVVRSICDYFFEDQSSDDDLEHVPPVISTPHHYLFSVYRD--LIFFCAVSTVET 75 (418)
T ss_pred CeeEEEEEcCCchhhhhHhhCCc---eeeeehHHHHHHhhhhccccccCCceecCCceeeeeeecc--CcEEEEEEeccC
Confidence 99999999999999999854410 111222222 222111 2233233443444444 3443 678888888777
Q ss_pred cHHHHHHHHHHHHHHHHHHhhhhchhHHHHhHHHHH---HHHHhCCEeeeccc
Q 033113 76 NELAYLECIHLFVEILDHFFSNVCELDLVFNFHKVC---DRIFISSSVTVSFC 125 (127)
Q Consensus 76 Nel~~le~I~~~ve~Ld~~f~nVcEldii~nf~k~~---DE~i~~G~v~e~~~ 125 (127)
-.|.+.||+|..++++..|||...|.-|..|+..+| |||+++|.++-|.+
T Consensus 76 pPL~~iefL~rv~dv~~eyFg~~s~~~Ik~N~~vv~ell~emiDnGfpl~tE~ 128 (418)
T KOG2740|consen 76 PPLMVIEFLHRVVDVLLEYFGGLSESKIKDNVVVVYELLDEMIDNGFPLVTEP 128 (418)
T ss_pred CChhHHHHHHHHHHHHHHHhcccCHhHhhcceeeHHHHHHHHHHcCCCcccCh
Confidence 799999999999999999999999999999999999 99999999987753
No 11
>KOG2635 consensus Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.86 E-value=0.00022 Score=61.16 Aligned_cols=114 Identities=21% Similarity=0.330 Sum_probs=92.3
Q ss_pred EEEEeecCCCCceeeecCCCCChHHHHHHHHHHhhhhcCCCCCccceEEeCCeEEEEEeeccEEEEEEecCCccHHHHHH
Q 033113 3 RFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRLVVNRDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNELAYLE 82 (127)
Q Consensus 3 ~~vli~n~~Gk~rl~K~Y~~~~~~~~~~~~~~v~~~v~~r~~~~~~~~~~~~~~ivYrrya~L~f~~~~d~~eNel~~le 82 (127)
-+.-+.+++||..+++=|..++-..-..+...--+++. ..++--|++-++++.||+..-.||+++++..+-|-|--|+
T Consensus 4 laa~i~t~~Gk~ivsRqf~~Msr~RIEgLl~aFpkLv~--~~~qhT~vEt~~VRYVYqP~d~lY~vLITtk~SNIleDl~ 81 (512)
T KOG2635|consen 4 LAASINTKTGKAIVSRQFREMSRSRIEGLLAAFPKLVS--AGKQHTFVETDSVRYVYQPLDNLYIVLITTKQSNILEDLE 81 (512)
T ss_pred EEEEEeecCCceeeehHhHhhhHHHHHHHHHHhHHhhc--cCCCccEEecccEEEEEEecccEEEEEEeccccchhhHHH
Confidence 45677899999999986655555444445555444443 3344669999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhhchhHHHHh-HHHHH--HHHHhCC
Q 033113 83 CIHLFVEILDHFFSNVCELDLVFN-FHKVC--DRIFISS 118 (127)
Q Consensus 83 ~I~~~ve~Ld~~f~nVcEldii~n-f~k~~--DE~i~~G 118 (127)
.++.|..+.-.|-.++.|+.|..| |+.++ ||++.=|
T Consensus 82 TL~Lfskvipey~~slde~eI~~~~FelifAFDEivsLG 120 (512)
T KOG2635|consen 82 TLRLFSKVIPEYCSSLDEKEILENAFELIFAFDEIVSLG 120 (512)
T ss_pred HHHHHHHhchhhhhhhhHHHHHHhhhhhhhccchhhhhc
Confidence 999999999999999999999876 45555 9999777
No 12
>PF15001 AP-5_subunit_s1: AP-5 complex subunit sigma-1
Probab=95.54 E-value=0.14 Score=39.55 Aligned_cols=67 Identities=15% Similarity=0.309 Sum_probs=50.4
Q ss_pred CeEEEEEeeccEEEEEEecCCccHHHHHHHHHHHHHHHHHHhhhhch-hHHHHhHHHHH---HHHHhCCEe
Q 033113 54 THKVIYRRYAGLFFSLCVDITDNELAYLECIHLFVEILDHFFSNVCE-LDLVFNFHKVC---DRIFISSSV 120 (127)
Q Consensus 54 ~~~ivYrrya~L~f~~~~d~~eNel~~le~I~~~ve~Ld~~f~nVcE-ldii~nf~k~~---DE~i~~G~v 120 (127)
...++.....++.|..+.|+.||-+..=.++..++..|-.+|..+.- ..+...-|.+. +..+=.|..
T Consensus 103 ~k~vvW~~v~~l~ftLVce~hEN~lLa~~~L~~~~~~l~~~~~~l~~~~e~l~k~d~i~aiL~~fLP~GQL 173 (189)
T PF15001_consen 103 PKIVVWLGVGSLCFTLVCEPHENRLLAENTLRLFIRHLLEHLKILSQPSEVLLKSDRILAILHRFLPHGQL 173 (189)
T ss_pred CcEEEeeccCCEEEEEEecCchhHHHHHHHHHHHHHHHHHHHHHhCcHHHhhhhHHHHHHHHHHhCCCCcE
Confidence 35678999999999999999999999999999999999888744322 33444555554 666655554
No 13
>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=93.60 E-value=1 Score=32.11 Aligned_cols=91 Identities=10% Similarity=0.129 Sum_probs=60.2
Q ss_pred eEEEEeecCCCCceeeecCCCCCh-HHHHHHHHHHhhhhcCC------CCCccceEEeCCeEEEEEeeccEEEEEEecCC
Q 033113 2 IRFILLQNRQGKTRLAKYYVPLED-SEKHKVEYEVHRLVVNR------DPKFTNFVEFRTHKVIYRRYAGLFFSLCVDIT 74 (127)
Q Consensus 2 I~~vli~n~~Gk~rl~K~Y~~~~~-~~~~~~~~~v~~~v~~r------~~~~~~~~~~~~~~ivYrrya~L~f~~~~d~~ 74 (127)
+.++++-|++|=+.+.=..+..+. .-+..+... |.....+ +...+-+..++++.++.-.+..|++.++++++
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 578999999999886644333222 222333322 3332221 23335577789999999999999999999999
Q ss_pred ccHHHHHHHHHHHHHHHHH
Q 033113 75 DNELAYLECIHLFVEILDH 93 (127)
Q Consensus 75 eNel~~le~I~~~ve~Ld~ 93 (127)
.|--+++.+=+.+.+.|..
T Consensus 96 aN~G~il~l~~~L~~~l~~ 114 (119)
T PF08923_consen 96 ANTGLILSLEEELAPILNE 114 (119)
T ss_dssp S-HHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHhHHHHHHHHHH
Confidence 9999988887777666643
No 14
>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=91.53 E-value=3.5 Score=35.04 Aligned_cols=76 Identities=8% Similarity=0.172 Sum_probs=53.2
Q ss_pred EEEeecCCCCceeeecCCCCChHHHHHHHHHHhhhhcC--CCCCccceEEeCCeEEEEEeeccEEEEEEecCCccHHHHH
Q 033113 4 FILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRLVVN--RDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNELAYL 81 (127)
Q Consensus 4 ~vli~n~~Gk~rl~K~Y~~~~~~~~~~~~~~v~~~v~~--r~~~~~~~~~~~~~~ivYrrya~L~f~~~~d~~eNel~~l 81 (127)
=++|+..-|||..+++ .++++-..+.+-+...++- .++..--.+.-++.++|+-.=..||++++....|++..+.
T Consensus 13 h~fIlS~AGKPIysr~---G~e~~l~~~~g~~~aiiS~~~~~~d~l~~i~~~~~~ivfl~r~pl~lv~vS~~~e~~~~l~ 89 (415)
T PF03164_consen 13 HFFILSSAGKPIYSRY---GDEDKLSSLMGVIQAIISFFQSNGDELRSIRAGDHRIVFLNRGPLILVAVSKTGESESQLR 89 (415)
T ss_pred eEEEECCCCceeEEec---CChHHHHHHHHHHHHHHHHHHhCCCcEEEEEeCCEEEEEEecCCEEEEEEcCCcCCHHHHH
Confidence 4789999999999998 4444444555444444331 1222233556799999999999999999999999865543
Q ss_pred H
Q 033113 82 E 82 (127)
Q Consensus 82 e 82 (127)
.
T Consensus 90 ~ 90 (415)
T PF03164_consen 90 K 90 (415)
T ss_pred H
Confidence 3
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=76.77 E-value=26 Score=25.38 Aligned_cols=92 Identities=20% Similarity=0.221 Sum_probs=49.7
Q ss_pred eEEEEeecCCCCceeee-cCCC-------CChHHHHHHHHHHhh------hhcCCCC-----CccceEE--eCCeEEE-E
Q 033113 2 IRFILLQNRQGKTRLAK-YYVP-------LEDSEKHKVEYEVHR------LVVNRDP-----KFTNFVE--FRTHKVI-Y 59 (127)
Q Consensus 2 I~~vli~n~~Gk~rl~K-~Y~~-------~~~~~~~~~~~~v~~------~v~~r~~-----~~~~~~~--~~~~~iv-Y 59 (127)
|..+.|+|+.|.-...+ |-.+ .+..+++.+-+-+|. ++++++. ..+.|-. -+.+|+. |
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 67899999999999997 5443 244556655544443 3333221 1233443 4688986 5
Q ss_pred EeeccEEEEEEecCCccHHHHHHHHHHHHHHHHHH
Q 033113 60 RRYAGLFFSLCVDITDNELAYLECIHLFVEILDHF 94 (127)
Q Consensus 60 rrya~L~f~~~~d~~eNel~~le~I~~~ve~Ld~~ 94 (127)
.--.++-|++++|.+... ..=++.+.+.++.-.|
T Consensus 81 eT~TGlKFvl~td~~~~~-~~~~l~~~~~~lY~dy 114 (142)
T PF04099_consen 81 ETPTGLKFVLITDPNVPS-LRDELLRIYYELYVDY 114 (142)
T ss_dssp E-TTS-EEEEEE-TTCCH-CHHHHHHHHHHHHHHH
T ss_pred EcCcCcEEEEEecCCCcc-HHHHHHHHHHHHHHHH
Confidence 557799999999998742 2222344444444333
No 16
>COG3322 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]
Probab=73.56 E-value=2.5 Score=34.71 Aligned_cols=23 Identities=13% Similarity=0.117 Sum_probs=19.7
Q ss_pred eEEEEeecCCCCceeeecCCCCC
Q 033113 2 IRFILLQNRQGKTRLAKYYVPLE 24 (127)
Q Consensus 2 I~~vli~n~~Gk~rl~K~Y~~~~ 24 (127)
..++|++|++|+++++|++++.+
T Consensus 104 ~d~vf~vd~~G~~vy~~~~d~~t 126 (295)
T COG3322 104 LDGVFVVDPSGKLVYSKLVDQET 126 (295)
T ss_pred ccEEEEECCCCCEEEEeeecccc
Confidence 36899999999999999997643
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=62.70 E-value=38 Score=21.67 Aligned_cols=48 Identities=8% Similarity=-0.009 Sum_probs=40.8
Q ss_pred eEEeCCeEEEEEeeccEEEEEEecCCccHHHHHHHHHHHHHHHHHHhh
Q 033113 49 FVEFRTHKVIYRRYAGLFFSLCVDITDNELAYLECIHLFVEILDHFFS 96 (127)
Q Consensus 49 ~~~~~~~~ivYrrya~L~f~~~~d~~eNel~~le~I~~~ve~Ld~~f~ 96 (127)
-++.+++.+.|..-.++.+++++|.+-..-....+|..+.+...+-|+
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 455889999999999999999999999999999999888777777765
No 18
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=56.91 E-value=97 Score=24.53 Aligned_cols=96 Identities=13% Similarity=0.131 Sum_probs=70.7
Q ss_pred CeEEEEeec-CCCCceeee---cCCCC-ChHHHHHHHHHHhhhhcCCCCCccceEEeCCeEEEEEeeccEEEEEEecCCc
Q 033113 1 MIRFILLQN-RQGKTRLAK---YYVPL-EDSEKHKVEYEVHRLVVNRDPKFTNFVEFRTHKVIYRRYAGLFFSLCVDITD 75 (127)
Q Consensus 1 MI~~vli~n-~~Gk~rl~K---~Y~~~-~~~~~~~~~~~v~~~v~~r~~~~~~~~~~~~~~ivYrrya~L~f~~~~d~~e 75 (127)
||+.-+|.= ++|-|.-+- ...+. +..+.++-.+.+++...+-++.+|. ++-|.+.+.|.--.++++.+..|.+=
T Consensus 1 mi~~T~I~RV~DGLPLa~s~d~~e~~~~s~~e~r~q~K~L~kkLs~~s~~r~S-ietg~f~fHfli~~~Vcylvicd~~y 79 (216)
T KOG0862|consen 1 MILLTLIARVRDGLPLAASTDDNEQSGDSLLEYRQQAKSLFKKLSQQSPTRCS-IETGPFVFHFLIESGVCYLVICDKSY 79 (216)
T ss_pred CceeEEEEEecCCcccccccCcccCCCchHHHHHHHHHHHHHhccCCCCcccc-cccCCeEEEEEecCCEEEEEEecCCC
Confidence 455444443 356554332 22233 4478888889999987755555555 45788999999999999999999999
Q ss_pred cHHHHHHHHHHHHHHHHHHhhh
Q 033113 76 NELAYLECIHLFVEILDHFFSN 97 (127)
Q Consensus 76 Nel~~le~I~~~ve~Ld~~f~n 97 (127)
..-.....+.-+.+-+++-+++
T Consensus 80 P~kLAF~YLedL~~EF~~~~~~ 101 (216)
T KOG0862|consen 80 PRKLAFSYLEDLAQEFDKSYGK 101 (216)
T ss_pred cHHHHHHHHHHHHHHHHHhccc
Confidence 8888889999988888888764
No 19
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=50.81 E-value=99 Score=22.83 Aligned_cols=85 Identities=16% Similarity=0.230 Sum_probs=50.0
Q ss_pred eEEEEeecCCCCceeee-cCCC-----CChHHHHHHHHHHhhh------hcCCCCCccceEEe--CCeEEEEEe-eccEE
Q 033113 2 IRFILLQNRQGKTRLAK-YYVP-----LEDSEKHKVEYEVHRL------VVNRDPKFTNFVEF--RTHKVIYRR-YAGLF 66 (127)
Q Consensus 2 I~~vli~n~~Gk~rl~K-~Y~~-----~~~~~~~~~~~~v~~~------v~~r~~~~~~~~~~--~~~~ivYrr-ya~L~ 66 (127)
|.++-|+|+.|.-.+.+ |..+ +.+++-|-.=+-+|.+ +++.+.+ -.|.-+ ..+|+.|=- =.+|+
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 77899999999999875 8753 2233334333444443 3322222 224433 457776444 55899
Q ss_pred EEEEecCCccHHHHHHHHHHHHH
Q 033113 67 FSLCVDITDNELAYLECIHLFVE 89 (127)
Q Consensus 67 f~~~~d~~eNel~~le~I~~~ve 89 (127)
|++.+|+.... +=|++|.+..
T Consensus 82 ~vl~Tdpk~~~--ir~vLq~IYs 102 (140)
T KOG3368|consen 82 FVLNTDPKAGS--IRDVLQYIYS 102 (140)
T ss_pred EEEecCCCccc--HHHHHHHHHH
Confidence 99999988763 3344444333
No 20
>PRK13190 putative peroxiredoxin; Provisional
Probab=46.09 E-value=35 Score=25.79 Aligned_cols=22 Identities=18% Similarity=0.304 Sum_probs=18.6
Q ss_pred eEEEEeecCCCCceeeecCCCC
Q 033113 2 IRFILLQNRQGKTRLAKYYVPL 23 (127)
Q Consensus 2 I~~vli~n~~Gk~rl~K~Y~~~ 23 (127)
+.+.+++|++|+.|....|...
T Consensus 117 ~p~~fiId~~G~I~~~~~~~~~ 138 (202)
T PRK13190 117 VRGVFIIDPNQIVRWMIYYPAE 138 (202)
T ss_pred EeEEEEECCCCEEEEEEEeCCC
Confidence 5788999999999999887643
No 21
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=43.56 E-value=1.2e+02 Score=21.89 Aligned_cols=90 Identities=14% Similarity=0.240 Sum_probs=52.0
Q ss_pred eEEEEeecCCCCceeeecCCC-C---ChHHHHHHH---HHHhhhhcCCCC--Cccc--eEEeCCeEE-EEEeeccEEEEE
Q 033113 2 IRFILLQNRQGKTRLAKYYVP-L---EDSEKHKVE---YEVHRLVVNRDP--KFTN--FVEFRTHKV-IYRRYAGLFFSL 69 (127)
Q Consensus 2 I~~vli~n~~Gk~rl~K~Y~~-~---~~~~~~~~~---~~v~~~v~~r~~--~~~~--~~~~~~~~i-vYrrya~L~f~~ 69 (127)
++.++|.|+.|-..+.+=+.. . +..|---+. ..|+....+-.+ ..+. .+..|+... +|+...++-|++
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 688999999999999987742 1 111111111 222222111111 1122 444566554 799999999999
Q ss_pred Ee-cCCccHHHHHHHHHHHHHHHHHH
Q 033113 70 CV-DITDNELAYLECIHLFVEILDHF 94 (127)
Q Consensus 70 ~~-d~~eNel~~le~I~~~ve~Ld~~ 94 (127)
+. ++.-|.+.- +|.+.+....|
T Consensus 83 ~~~k~t~na~~q---l~kiY~lYsdY 105 (134)
T COG5122 83 VAEKRTVNALFQ---LQKIYSLYSDY 105 (134)
T ss_pred EecCCchhHHHH---HHHHHHHHHHH
Confidence 99 566664433 55566666555
No 22
>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=42.75 E-value=50 Score=24.89 Aligned_cols=21 Identities=29% Similarity=0.558 Sum_probs=17.6
Q ss_pred eEEEEeecCCCCceeeecCCC
Q 033113 2 IRFILLQNRQGKTRLAKYYVP 22 (127)
Q Consensus 2 I~~vli~n~~Gk~rl~K~Y~~ 22 (127)
+++.+++|++|+.|....|..
T Consensus 117 ~r~~fiID~~G~I~~~~~~~~ 137 (203)
T cd03016 117 VRAVFIIDPDKKIRLILYYPA 137 (203)
T ss_pred eeEEEEECCCCeEEEEEecCC
Confidence 357899999999999988853
No 23
>KOG0859 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=40.25 E-value=1.9e+02 Score=22.92 Aligned_cols=76 Identities=12% Similarity=0.074 Sum_probs=45.5
Q ss_pred cCCCCceeeecCCCCChHHHHHHHHHHhhhhcCCCC-CccceEEeCCeEEEEEeeccEEEEEEecCCccHHHHHHHHHHH
Q 033113 9 NRQGKTRLAKYYVPLEDSEKHKVEYEVHRLVVNRDP-KFTNFVEFRTHKVIYRRYAGLFFSLCVDITDNELAYLECIHLF 87 (127)
Q Consensus 9 n~~Gk~rl~K~Y~~~~~~~~~~~~~~v~~~v~~r~~-~~~~~~~~~~~~ivYrrya~L~f~~~~d~~eNel~~le~I~~~ 87 (127)
=..|-+.|++|=.... .-..+.+++-+++.+.++ +. -...+++++.|.+--++.+++++|.+..--.-..|+...
T Consensus 8 VARGTvvLaeft~~~g--Nf~sva~qiL~klp~~~n~k~--tYs~d~y~Fh~l~~dg~tylcvadds~gR~ipfaFLe~I 83 (217)
T KOG0859|consen 8 VARGTVILAEFTEFSG--NFSSIAAQILQKLPSSSNSKF--TYSCDGYTFHYLVEDGLTYLCVADDSAGRQIPFAFLERI 83 (217)
T ss_pred EecceEEEEeeeeccC--CHHHHHHHHHHhCCCCCCCce--EEecCCeEEEEEEeCCeEEEEEEeccccccccHHHHHHH
Confidence 3579999999643111 122233444444332221 21 123589999999999999999999876655544444433
Q ss_pred H
Q 033113 88 V 88 (127)
Q Consensus 88 v 88 (127)
-
T Consensus 84 k 84 (217)
T KOG0859|consen 84 K 84 (217)
T ss_pred H
Confidence 3
No 24
>PRK13599 putative peroxiredoxin; Provisional
Probab=36.90 E-value=49 Score=25.49 Aligned_cols=21 Identities=29% Similarity=0.659 Sum_probs=17.7
Q ss_pred eEEEEeecCCCCceeeecCCC
Q 033113 2 IRFILLQNRQGKTRLAKYYVP 22 (127)
Q Consensus 2 I~~vli~n~~Gk~rl~K~Y~~ 22 (127)
+++++|+|++|+.|.+-+|..
T Consensus 119 ~R~tfIID~dG~Ir~~~~~p~ 139 (215)
T PRK13599 119 VRAVFIVDDKGTIRLIMYYPQ 139 (215)
T ss_pred eeEEEEECCCCEEEEEEEcCC
Confidence 478999999999999976653
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=35.49 E-value=1.2e+02 Score=22.59 Aligned_cols=90 Identities=11% Similarity=0.148 Sum_probs=42.3
Q ss_pred CeEEEEeecCCCCceeeec-C-CCCChHHHHHHHHHHhhhhcCCC--CCccceEEeC-------CeEEEEEe--eccEEE
Q 033113 1 MIRFILLQNRQGKTRLAKY-Y-VPLEDSEKHKVEYEVHRLVVNRD--PKFTNFVEFR-------THKVIYRR--YAGLFF 67 (127)
Q Consensus 1 MI~~vli~n~~Gk~rl~K~-Y-~~~~~~~~~~~~~~v~~~v~~r~--~~~~~~~~~~-------~~~ivYrr--ya~L~f 67 (127)
|+.-+-||.+||+....-- . +..++.+-.++++++...-++|+ ...++|++.. +++..|.- =--|||
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 8888999999999875311 0 12455566677777766533333 2236777765 55555543 235777
Q ss_pred EEEecCCccHHHHHHHHHHHHHHHHHHh
Q 033113 68 SLCVDITDNELAYLECIHLFVEILDHFF 95 (127)
Q Consensus 68 ~~~~d~~eNel~~le~I~~~ve~Ld~~f 95 (127)
++.--+ -.||+=+---++||.-+
T Consensus 81 VvTyae-----qsleLn~EAe~~L~lal 103 (148)
T PF09201_consen 81 VVTYAE-----QSLELNQEAEQTLDLAL 103 (148)
T ss_dssp EEEESS-------HHHHHHHHHHHHHHH
T ss_pred EEEecc-----ccchhhHHHHHHHHHHH
Confidence 776654 23444444555555443
No 26
>KOG0781 consensus Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=34.64 E-value=84 Score=28.18 Aligned_cols=67 Identities=12% Similarity=0.083 Sum_probs=39.3
Q ss_pred CeEEEEeecCCCCceeeecCCCCChHHHHHHHHHHhhh-hcCCCCCccceEEeCCeEEEEEeecc--EEEEEEe
Q 033113 1 MIRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRL-VVNRDPKFTNFVEFRTHKVIYRRYAG--LFFSLCV 71 (127)
Q Consensus 1 MI~~vli~n~~Gk~rl~K~Y~~~~~~~~~~~~~~v~~~-v~~r~~~~~~~~~~~~~~ivYrrya~--L~f~~~~ 71 (127)
||..+.||++.|......-=.....++ .+..+++. ++++.....+ ++++.+++-|..-.. +.|+++-
T Consensus 1 Mld~faIFtkgG~vLw~~~~~~~~~~~---~in~lI~~~ll~er~~~~~-~~~~~yTlk~q~~N~~~lvfvvvf 70 (587)
T KOG0781|consen 1 MLDQFAIFTKGGLVLWCYQEVGDNLKG---PINALIRSVLLSERGGVNS-FTFEAYTLKYQLDNQYSLVFVVVF 70 (587)
T ss_pred CcceeeeecCCcEEEEEecccchhccc---hHHHHHHHHHHHhhcCccc-CchhheeEeeeecCCccEEEEEEE
Confidence 899999999999987554222233333 33344443 2333333233 678889998887543 4444444
No 27
>PRK13191 putative peroxiredoxin; Provisional
Probab=32.08 E-value=87 Score=24.05 Aligned_cols=21 Identities=29% Similarity=0.622 Sum_probs=18.2
Q ss_pred eEEEEeecCCCCceeeecCCC
Q 033113 2 IRFILLQNRQGKTRLAKYYVP 22 (127)
Q Consensus 2 I~~vli~n~~Gk~rl~K~Y~~ 22 (127)
+++.+|+|++|+.|..-+|..
T Consensus 124 ~r~tfIID~~G~Ir~~~~~~~ 144 (215)
T PRK13191 124 VRAVFIVDDKGTVRLILYYPM 144 (215)
T ss_pred eEEEEEECCCCEEEEEEecCC
Confidence 478899999999999988863
No 28
>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=30.58 E-value=1.9e+02 Score=20.09 Aligned_cols=21 Identities=19% Similarity=0.357 Sum_probs=17.0
Q ss_pred eEEEEeecCCCCcee--eecCCC
Q 033113 2 IRFILLQNRQGKTRL--AKYYVP 22 (127)
Q Consensus 2 I~~vli~n~~Gk~rl--~K~Y~~ 22 (127)
+.+++++|++|+++. ++.+..
T Consensus 50 ~d~~~~~d~~g~~~~~~~~~~~~ 72 (161)
T PF05228_consen 50 LDLIFILDPDGRVLYSSSKGYDF 72 (161)
T ss_pred ccEEEEEcCCCCEEEEeccCccc
Confidence 468999999999998 666553
No 29
>PF13867 SAP30_Sin3_bdg: Sin3 binding region of histone deacetylase complex subunit SAP30; PDB: 2LD7_A.
Probab=29.83 E-value=66 Score=19.47 Aligned_cols=22 Identities=23% Similarity=0.425 Sum_probs=15.8
Q ss_pred HHHHHHHHhhh--hchhHHHHhHH
Q 033113 87 FVEILDHFFSN--VCELDLVFNFH 108 (127)
Q Consensus 87 ~ve~Ld~~f~n--VcEldii~nf~ 108 (127)
+++++.++|.+ |.|.|+|-+|-
T Consensus 26 La~~V~kHF~s~~v~E~evI~~Fl 49 (53)
T PF13867_consen 26 LANAVRKHFNSQPVDENEVIANFL 49 (53)
T ss_dssp HHHHHHHHHTT----HHHHHHHHH
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHH
Confidence 46677888864 89999999984
No 30
>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=29.17 E-value=1.1e+02 Score=22.12 Aligned_cols=35 Identities=9% Similarity=-0.054 Sum_probs=20.6
Q ss_pred EEEEeecCCCCceeeecCCCCChHHHHHHHHHHhh
Q 033113 3 RFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHR 37 (127)
Q Consensus 3 ~~vli~n~~Gk~rl~K~Y~~~~~~~~~~~~~~v~~ 37 (127)
...+++|++|+.+.......+.....+++.+.+-+
T Consensus 121 p~~~lID~~G~I~~~~~~~~~~~~~~~~il~~l~~ 155 (173)
T cd03015 121 RGTFIIDPEGIIRHITVNDLPVGRSVDETLRVLDA 155 (173)
T ss_pred eEEEEECCCCeEEEEEecCCCCCCCHHHHHHHHHH
Confidence 46899999998887663322222233445555533
No 31
>KOG0854 consensus Alkyl hydroperoxide reductase, thiol specific antioxidant and related enzymes [Posttranslational modification, protein turnover, chaperones]
Probab=29.04 E-value=52 Score=25.74 Aligned_cols=35 Identities=14% Similarity=0.239 Sum_probs=25.0
Q ss_pred eEEEEeecCCCCceeeecCCCCChHHHHHHHHHHh
Q 033113 2 IRFILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVH 36 (127)
Q Consensus 2 I~~vli~n~~Gk~rl~K~Y~~~~~~~~~~~~~~v~ 36 (127)
++++++++++-|.||+=+|...+-..-.++.+-|-
T Consensus 131 ~Ravfvi~pdkKirLs~lYP~ttGRN~dEiLRvid 165 (224)
T KOG0854|consen 131 VRAVFVIDPDKKIRLSFLYPSTTGRNFDEILRVID 165 (224)
T ss_pred EEEEEEECCCceEEEEEEcccccCcCHHHHHHHHH
Confidence 68999999999999999997643333333444443
No 32
>PRK13189 peroxiredoxin; Provisional
Probab=27.61 E-value=1.1e+02 Score=23.58 Aligned_cols=20 Identities=25% Similarity=0.544 Sum_probs=17.2
Q ss_pred eEEEEeecCCCCceeeecCC
Q 033113 2 IRFILLQNRQGKTRLAKYYV 21 (127)
Q Consensus 2 I~~vli~n~~Gk~rl~K~Y~ 21 (127)
+++.+|+|++|+.|....|.
T Consensus 126 ~r~tfIID~~G~Ir~~~~~~ 145 (222)
T PRK13189 126 VRAVFIIDPKGIIRAILYYP 145 (222)
T ss_pred eeEEEEECCCCeEEEEEecC
Confidence 46789999999999888775
No 33
>PTZ00253 tryparedoxin peroxidase; Provisional
Probab=27.15 E-value=1.1e+02 Score=22.82 Aligned_cols=20 Identities=15% Similarity=0.139 Sum_probs=16.3
Q ss_pred eEEEEeecCCCCceeeecCC
Q 033113 2 IRFILLQNRQGKTRLAKYYV 21 (127)
Q Consensus 2 I~~vli~n~~Gk~rl~K~Y~ 21 (127)
.++.+|+|++|+.|....+.
T Consensus 127 ~r~~fiID~~G~i~~~~~~~ 146 (199)
T PTZ00253 127 YRGLFIIDPKGMLRQITVND 146 (199)
T ss_pred EEEEEEECCCCEEEEEEecC
Confidence 36789999999999876664
No 34
>PRK15000 peroxidase; Provisional
Probab=24.32 E-value=1.4e+02 Score=22.57 Aligned_cols=20 Identities=20% Similarity=0.117 Sum_probs=17.0
Q ss_pred eEEEEeecCCCCceeeecCC
Q 033113 2 IRFILLQNRQGKTRLAKYYV 21 (127)
Q Consensus 2 I~~vli~n~~Gk~rl~K~Y~ 21 (127)
+++.+++|++|+.|....+.
T Consensus 125 ~r~tfiID~~G~I~~~~~~~ 144 (200)
T PRK15000 125 LRGSFLIDANGIVRHQVVND 144 (200)
T ss_pred EeEEEEECCCCEEEEEEecC
Confidence 57889999999999987664
No 35
>PTZ00137 2-Cys peroxiredoxin; Provisional
Probab=24.06 E-value=1.2e+02 Score=24.30 Aligned_cols=21 Identities=19% Similarity=0.229 Sum_probs=17.5
Q ss_pred eEEEEeecCCCCceeeecCCC
Q 033113 2 IRFILLQNRQGKTRLAKYYVP 22 (127)
Q Consensus 2 I~~vli~n~~Gk~rl~K~Y~~ 22 (127)
+.+.+|+|++|+.|.+.-|..
T Consensus 188 ~R~tFIID~dG~I~~~~~~~~ 208 (261)
T PTZ00137 188 HRASVLVDKAGVVKHVAVYDL 208 (261)
T ss_pred ecEEEEECCCCEEEEEEEeCC
Confidence 467899999999999886653
No 36
>PRK13728 conjugal transfer protein TrbB; Provisional
Probab=23.51 E-value=1.6e+02 Score=22.47 Aligned_cols=35 Identities=11% Similarity=-0.063 Sum_probs=26.2
Q ss_pred EEEeecCCCCceeeecCCCCChHHHHHHHHHHhhh
Q 033113 4 FILLQNRQGKTRLAKYYVPLEDSEKHKVEYEVHRL 38 (127)
Q Consensus 4 ~vli~n~~Gk~rl~K~Y~~~~~~~~~~~~~~v~~~ 38 (127)
..+++|++|+.+...++...+.++-.+.+.++.+.
T Consensus 139 ttfLId~~G~i~~~~~~G~~~~~~L~~~I~~ll~~ 173 (181)
T PRK13728 139 TTFLVNVNTLEALPLLQGATDAAGFMARMDTVLQM 173 (181)
T ss_pred eEEEEeCCCcEEEEEEECCCCHHHHHHHHHHHHhh
Confidence 35889999999887788887777666666665554
No 37
>COG0450 AhpC Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=21.94 E-value=86 Score=24.39 Aligned_cols=33 Identities=15% Similarity=0.021 Sum_probs=23.6
Q ss_pred eEEEEeecCCCCceeeecCCCC---ChHHHHHHHHH
Q 033113 2 IRFILLQNRQGKTRLAKYYVPL---EDSEKHKVEYE 34 (127)
Q Consensus 2 I~~vli~n~~Gk~rl~K~Y~~~---~~~~~~~~~~~ 34 (127)
.++++|.|++|.+|..-.|... +..|--|.++.
T Consensus 124 ~R~~FIIDp~g~ir~~~v~~~~iGRn~dEilR~idA 159 (194)
T COG0450 124 LRGTFIIDPDGVIRHILVNPLTIGRNVDEILRVIDA 159 (194)
T ss_pred eeEEEEECCCCeEEEEEEecCCCCcCHHHHHHHHHH
Confidence 4789999999999999888643 34444444443
No 38
>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=21.04 E-value=93 Score=19.07 Aligned_cols=18 Identities=28% Similarity=0.353 Sum_probs=15.1
Q ss_pred cHHHHHHHHHHHHHHHHH
Q 033113 76 NELAYLECIHLFVEILDH 93 (127)
Q Consensus 76 Nel~~le~I~~~ve~Ld~ 93 (127)
+-|.+++|++.|-++|.-
T Consensus 6 ~~L~v~~Fl~~F~~~L~L 23 (61)
T PF02791_consen 6 DLLMVWEFLNTFGEVLGL 23 (61)
T ss_pred HHHHHHHHHHHHHHHHcC
Confidence 458899999999998864
Done!